Palau eDNA Report Template

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Affiliation

Author name 1

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Published

May 7, 2024

1 Document Purpose

This document is a template for analysis and reporting eDNA results. This file is a Quarto document (a newer version of a Rmarkdown file Intro to a Quarto doc) that can be opened in Rstudio and serve two purposes: 1) run code and 2) build a html (or pdf) report document.

The authors intended this file along with the other folders & files within this project to document analysis steps, make analyses reproducible, and make future analyses smoother and quicker to run. See the Quarto Website for a more in depth introduction to Quarto docs. The “Document Purpose & Description” section can be deleted when creating a new analysis.

1.1 Document Components

  1. YAML (yet another markdown language) header - the code contained at the top of this document bounded by a set of --- marks. This is a place to store document metadata and instructions for how the rest of the quarto doc should run code chunks and format rendered documents. See here for more information –> Authoring Docs and YAML HTML Options. We currently have the YAML set so when you Render this document a self-contained .html document will be created, this file format and formatting options can be further customized.

  2. Code chunks - code chunks are like mini code scripts. In a quarto doc you can run these individually by clicking on the green arrow/triangle in the upper right corner of the chunk OR using your “run code” shortcut. These chunks are allow to user to write text in between code, and provide instructions on how the code should be incorporated into the rendered document, including how figures should be displayed. See here for more information –> Code chunk options (work in both quarto and Rmarkdown docs)

  3. Markdown - This bullet list is written in markdown. Markdown is a simple text and formatting language. Use this to write text in the rendered report document. Here is a quick guide to markdown syntax –> Markdown cheat sheet. You can also use values and/or objects generated in your code to populate in your markdown text, see here —> How to use a code value in markdown text

1.2 Code Chunk Example - Run Code

The primary function of this document is to run code. Below is an example of a code chunk that runs R code. These are where data cleaning and analysis steps are contained. In Rstudio you can run code several ways:

Code
# Code chunk example

# The coding language is indicated in the very first line, within the curly brackets {}. 
# Use `#| ` to set options for the individual code chunk below the first line of the code chunk.

# A code chunk execute option `echo: true` enables the printing of code output in rendered report 

# here is example R code. To write comments within a code chunk, use a # at the beginning of the line, lines with # will not be run within a code chunk.
test <- 1 + 1
test_2 <- test * 6
test_2
[1] 12
  1. line-by-line (just like a normal .R file)

  2. chunk-by-chunk (press the green right-facing triangle at the top right corner of the code chunk)

  1. all code top to bottom ()

1.3 Render Quarto Docs - Build Report Doc

The secondary function of this document is to build a report document. This requires all the code in the Quarto document to run cleanly without errors. To build the report, click the Render button shown below. This will start a multistage process that runs all the code and markdown sequentially and formats it based on the YAML header and code chunk execute options.

There are two ways to alter/customize the resulting report:

  1. The YAML header (described above). For example, to set the default execution options for all code chunks, you can add options in the YAML (execute:)

  1. Set run options for individual code chunks. More details here –> https://quarto.org/docs/computations/execution-options.html

The final template .html product will look something like this:

2 Analysis Template

Below is the code required for eDNA analysis

2.1 Setup

Load packages

We used the renv package to manage & record package versions. This records the version of R, package versions, and their dependencies into a file renv.lock at the root of this .Rproj. The purpose of this is to allow users on different computer setups and in the future to reproduce the results of this project in the same way. This is because different package versions can behave differently version to version, and even introduce errors or produced different results. By using the same exact set of package versions that the authors used to write the code, the same results can be reproduced and prevent unintended errors.

Renv creates a separate custom project library that is separate from the system library typically used when the library() function is called. This means that when you recreate the renv project library by calling renv::restore() you will likely need to install many packages. Many may be already installed in your system library, but they will need to be installed again into this custom renv project library with the exact version recorded in the renv.lock file. All files, folders, and scripts within the .Rproj will share the renv project library.

For more information about renv and how to add/update the renv project library -> .

Warning

Although this package management strategy is meant to reduce errors among future users, it is not perfect. The authors found that the renv project library could not yet be recreated on a M1 chip Apple computer (2023-10).

Create paths to folders

Set analysis date

Load data

2.2 Clean & save data

Clean & organize data

The code chunk below “clean-data” is separated into its own ./scripts/clean_data.R file and sourced by calling source(file.path(dir_scripts, clean_data.R) here. If you are looking save space in this analysis document, or want to reuse this exact same data cleaning protocol in different analysis document. The same goes for “create-nearshore-offshore-data” and “create-near-offshore-species-list” chunks, they could be their own scripts or be added to a clean_data script. If you choose to do this, the “example-source-clean-data” chunk below can be used.

loaded exsisting clean data

Create Nearshore & Offshore dataframes (or load if they already exist)

Create Nearshore & Offshore species dataframes (or load if they already exist)

2.3 Data Analysis

Unique Species

Unique Species - nearshore

Unique Species - offshore

Unique Genera

Unique Families

Transform data to Phyloseq Object

Explore Components of Phyloseq Object (if needed)

Subset Phyloseq Samples - Keep Environmental Samples Only

Subset Phyloseq Environmental Samples - ESVs with marine fish and mammal annotations

Environmental Marine Samples With More Than 10,000 Sequences

Standardize number of reads to the median sequencing depth

Subset taxa

Subset created successfully
Subset created successfully
'Chondrichthyes' not found in the Class column

3 Visualizing

Barplot - Families - Environmental Samples (excluding Controls)

Barplot - Normalized Environmental Samples & Marine ESVs

  • Family

  • Order

Heatmap - Normalized Environmental Samples & Marine ESVs

  • Phylum

Barplot - Alternative formats

  • Family

  • Family facet wrap

Richness plots

Ordinations

Code
Fig_ord_near_off <- po +
  facet_wrap(~Near_or_Offshore) +
  scale_color_manual(values = zone_colors,
                     breaks = c("SHR", "LGN", "FRR", "AFZ", "DFZ", "NMS"),
                     guide = guide_legend(override.aes = list(size = 3, shape = c(16,16,16,17,17,17)))) +
  guides(shape = guide_legend(override.aes = list(size = 3, shape = c(1,2)))) +
  theme_light() +
  labs(shape = "Region") +
  coord_fixed()

Fig_ord_near_off

Code
ggsave(plot = Fig_ord_near_off, 
       device = "png", 
       filename = file.path("products/figures/Fig_ord_near_offshore_rv.png"),
       dpi = 600,
       width = 7,
       height = 3.5,
       units = "in")

### USE for Prelim Report

Marine Actinopteri (Bony Fish) bar plot

Marine Mammals

quartz_off_screen 
                2 

Marine Chondrichthyes (Sharks & Rays)

'physeq_std_Con' does not exist.

Top10

Taxonomy Table:     [10 taxa by 7 taxonomic ranks]:
           Kingdom     Phylum     Class         Order             
ESV_034098 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_033752 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_041947 "Eukaryota" "Chordata" "Actinopteri" "Myctophiformes"  
ESV_000975 "Eukaryota" "Chordata" "Actinopteri" "Centrarchiformes"
ESV_042017 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_000044 "Eukaryota" "Chordata" "Actinopteri" "Carangiformes"   
ESV_000892 "Eukaryota" "Chordata" "Actinopteri" "Carangiformes"   
ESV_027356 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_033648 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_001029 "Eukaryota" "Chordata" "Actinopteri" "Scombriformes"   
           Family          Genus           Species                    
ESV_034098 "Exocoetidae"   "Cheilopogon"   NA                         
ESV_033752 "Exocoetidae"   "Exocoetus"     "Exocoetus volitans"       
ESV_041947 "Myctophidae"   "Myctophum"     "Myctophum lychnobium"     
ESV_000975 "Kyphosidae"    "Kyphosus"      NA                         
ESV_042017 "Exocoetidae"   "Prognichthys"  "Prognichthys sealei"      
ESV_000044 "Carangidae"    "Decapterus"    "Decapterus macarellus"    
ESV_000892 "Carangidae"    "Selar"         "Selar crumenophthalmus"   
ESV_027356 "Exocoetidae"   NA              NA                         
ESV_033648 "Hemiramphidae" "Oxyporhamphus" "Oxyporhamphus micropterus"
ESV_001029 "Scombridae"    "Katsuwonus"    "Katsuwonus pelamis"       
[1] "Control_or_Envtl"   "Near_or_Offshore"   "Date"              
[4] "Cardinal_direction" "Zone"               "Station"           
[7] "Replicate"          "Duplicate"         
[1] "Control_or_Envtl"   "Near_or_Offshore"   "Date"              
[4] "Cardinal_direction" "Zone"               "Station"           
[7] "Replicate"          "Duplicate"         

###Subsetting and pruning Nearshore and Offshore sample sets

[1] "Control_or_Envtl"   "Near_or_Offshore"   "Date"              
[4] "Cardinal_direction" "Zone"               "Station"           
[7] "Replicate"          "Duplicate"         
Taxonomy Table:     [10 taxa by 7 taxonomic ranks]:
           Kingdom     Phylum     Class         Order             
ESV_034098 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_033752 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_041947 "Eukaryota" "Chordata" "Actinopteri" "Myctophiformes"  
ESV_000975 "Eukaryota" "Chordata" "Actinopteri" "Centrarchiformes"
ESV_042017 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_000044 "Eukaryota" "Chordata" "Actinopteri" "Carangiformes"   
ESV_000892 "Eukaryota" "Chordata" "Actinopteri" "Carangiformes"   
ESV_027356 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_033648 "Eukaryota" "Chordata" "Actinopteri" "Beloniformes"    
ESV_001029 "Eukaryota" "Chordata" "Actinopteri" "Scombriformes"   
           Family          Genus           Species                    
ESV_034098 "Exocoetidae"   "Cheilopogon"   NA                         
ESV_033752 "Exocoetidae"   "Exocoetus"     "Exocoetus volitans"       
ESV_041947 "Myctophidae"   "Myctophum"     "Myctophum lychnobium"     
ESV_000975 "Kyphosidae"    "Kyphosus"      NA                         
ESV_042017 "Exocoetidae"   "Prognichthys"  "Prognichthys sealei"      
ESV_000044 "Carangidae"    "Decapterus"    "Decapterus macarellus"    
ESV_000892 "Carangidae"    "Selar"         "Selar crumenophthalmus"   
ESV_027356 "Exocoetidae"   NA              NA                         
ESV_033648 "Hemiramphidae" "Oxyporhamphus" "Oxyporhamphus micropterus"
ESV_001029 "Scombridae"    "Katsuwonus"    "Katsuwonus pelamis"       
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 58 samples ]
sample_data() Sample Data:       [ 58 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 88 samples ]
sample_data() Sample Data:       [ 88 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 1777 taxa and 58 samples ]
sample_data() Sample Data:       [ 58 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 1777 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 577 taxa and 88 samples ]
sample_data() Sample Data:       [ 88 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 577 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 1777 taxa and 58 samples ]
sample_data() Sample Data:       [ 58 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 1777 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 577 taxa and 88 samples ]
sample_data() Sample Data:       [ 88 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 577 taxa by 7 taxonomic ranks ]

###Subset by Zones

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 19 samples ]
sample_data() Sample Data:       [ 19 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 19 samples ]
sample_data() Sample Data:       [ 19 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 20 samples ]
sample_data() Sample Data:       [ 20 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 20 samples ]
sample_data() Sample Data:       [ 20 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 18 samples ]
sample_data() Sample Data:       [ 18 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 2297 taxa and 50 samples ]
sample_data() Sample Data:       [ 50 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 2297 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 748 taxa and 19 samples ]
sample_data() Sample Data:       [ 19 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 748 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 600 taxa and 19 samples ]
sample_data() Sample Data:       [ 19 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 600 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 663 taxa and 20 samples ]
sample_data() Sample Data:       [ 20 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 663 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 163 taxa and 20 samples ]
sample_data() Sample Data:       [ 20 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 163 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 110 taxa and 18 samples ]
sample_data() Sample Data:       [ 18 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 110 taxa by 7 taxonomic ranks ]
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 377 taxa and 50 samples ]
sample_data() Sample Data:       [ 50 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 377 taxa by 7 taxonomic ranks ]

###Family counts of physeq_mar_std object (sf)

 [1] "Exocoetidae"      "Scombridae"       "Myctophidae"      "Carangidae"      
 [5] "Salmonidae"       "Engraulidae"      "Lethrinidae"      "Kyphosidae"      
 [9] "Acanthuridae"     NA                 "Leuciscidae"      "Atherinidae"     
[13] "Nomeidae"         "Clupeidae"        "Gerreidae"        "Hemiramphidae"   
[17] "Gobiidae"         "Lutjanidae"       "Holocentridae"    "Belonidae"       
[21] "Pomacentridae"    "Siganidae"        "Mullidae"         "Istiophoridae"   
[25] "Labridae"         "Gempylidae"       "Apogonidae"       "Eleotridae"      
[29] "Cottidae"         "Haemulidae"       "Mugilidae"        "Fundulidae"      
[33] "Sphyraenidae"     "Ephippidae"       "Balistidae"       "Muraenidae"      
[37] "Gobionidae"       "Cyprinidae"       "Poeciliidae"      "Tetraodontidae"  
[41] "Moronidae"        "Pomacanthidae"    "Bramidae"         "Chaetodontidae"  
[45] "Serranidae"       "Percidae"         "Blenniidae"       "Monacanthidae"   
[49] "Pseudochromidae"  "Phosichthyidae"   "Callionymidae"    "Chanidae"        
[53] "Delphinidae"      "Emmelichthyidae"  "Leiognathidae"    "Cichlidae"       
[57] "Cyprinodontidae"  "Sparidae"         "Synodontidae"     "Tripterygiidae"  
[61] "Gonostomatidae"   "Congridae"        "Monodactylidae"   "Nemacheilidae"   
[65] "Moringuidae"      "Platycephalidae"  "Toxotidae"        "Ophichthidae"    
[69] "Catostomidae"     "Scorpaenidae"     "Caracanthidae"    "Diodontidae"     
[73] "Bregmacerotidae"  "Bythitidae"       "Fistulariidae"    "Zenarchopteridae"
[77] "Echeneidae"       "Trichonotidae"    "Coryphaenidae"    "Clinidae"        
[81] "Albulidae"        "Schindleriidae"   "Soleidae"         "Nemipteridae"    
[85] "Antennariidae"    "Megalopidae"      "Isonidae"         "Pinguipedidae"   
[89] "Priacanthidae"    "Cirrhitidae"      "Ophidiidae"      
 [1] "Exocoetidae"      "Scombridae"       "Carangidae"       "Salmonidae"      
 [5] "Engraulidae"      "Lethrinidae"      "Kyphosidae"       "Acanthuridae"    
 [9] "Leuciscidae"      "Atherinidae"      "Clupeidae"        "Gerreidae"       
[13] "Hemiramphidae"    "Gobiidae"         "Lutjanidae"       "Holocentridae"   
[17] "Belonidae"        "Pomacentridae"    "Siganidae"        "Mullidae"        
[21] "Istiophoridae"    "Labridae"         "Apogonidae"       "Eleotridae"      
[25] "Haemulidae"       "Mugilidae"        NA                 "Myctophidae"     
[29] "Sphyraenidae"     "Balistidae"       "Muraenidae"       "Gobionidae"      
[33] "Poeciliidae"      "Tetraodontidae"   "Pomacanthidae"    "Chaetodontidae"  
[37] "Serranidae"       "Percidae"         "Cottidae"         "Blenniidae"      
[41] "Monacanthidae"    "Pseudochromidae"  "Callionymidae"    "Chanidae"        
[45] "Emmelichthyidae"  "Cyprinidae"       "Leiognathidae"    "Cyprinodontidae" 
[49] "Sparidae"         "Synodontidae"     "Tripterygiidae"   "Congridae"       
[53] "Ephippidae"       "Monodactylidae"   "Moringuidae"      "Platycephalidae" 
[57] "Toxotidae"        "Ophichthidae"     "Fundulidae"       "Scorpaenidae"    
[61] "Caracanthidae"    "Diodontidae"      "Bregmacerotidae"  "Bythitidae"      
[65] "Fistulariidae"    "Zenarchopteridae" "Echeneidae"       "Trichonotidae"   
[69] "Albulidae"        "Schindleriidae"   "Soleidae"         "Nemipteridae"    
[73] "Antennariidae"    "Megalopidae"      "Isonidae"         "Pinguipedidae"   
[77] "Priacanthidae"    "Ophidiidae"      
 [1] "Exocoetidae"    "Scombridae"     "Myctophidae"    "Carangidae"    
 [5] "Salmonidae"     "Kyphosidae"     NA               "Leuciscidae"   
 [9] "Nomeidae"       "Hemiramphidae"  "Holocentridae"  "Belonidae"     
[13] "Siganidae"      "Mullidae"       "Istiophoridae"  "Gempylidae"    
[17] "Cottidae"       "Mugilidae"      "Fundulidae"     "Sphyraenidae"  
[21] "Acanthuridae"   "Gobiidae"       "Ephippidae"     "Gobionidae"    
[25] "Cyprinidae"     "Poeciliidae"    "Moronidae"      "Gerreidae"     
[29] "Bramidae"       "Clupeidae"      "Engraulidae"    "Labridae"      
[33] "Blenniidae"     "Phosichthyidae" "Callionymidae"  "Delphinidae"   
[37] "Cichlidae"      "Sparidae"       "Gonostomatidae" "Muraenidae"    
[41] "Nemacheilidae"  "Lutjanidae"     "Balistidae"     "Catostomidae"  
[45] "Coryphaenidae"  "Clinidae"       "Tetraodontidae" "Pomacentridae" 
[49] "Pomacanthidae"  "Isonidae"       "Serranidae"     "Cirrhitidae"   

Genus counts of physeq_mar_std object (sf)

  [1] "Cheilopogon"        "Thunnus"            "Myctophum"         
  [4] "Exocoetus"          "Decapterus"         "Katsuwonus"        
  [7] "Oncorhynchus"       NA                   "Prognichthys"      
 [10] "Encrasicholina"     "Lethrinus"          "Selar"             
 [13] "Kyphosus"           "Ctenochaetus"       "Bolinichthys"      
 [16] "Hypoatherina"       "Cubiceps"           "Spratelloides"     
 [19] "Gerres"             "Symbolophorus"      "Acanthurus"        
 [22] "Oxyporhamphus"      "Callogobius"        "Caesio"            
 [25] "Myripristis"        "Tylosurus"          "Pterocaesio"       
 [28] "Lutjanus"           "Hemiramphus"        "Hygophum"          
 [31] "Pomacentrus"        "Siganus"            "Caranx"            
 [34] "Monotaxis"          "Mulloidichthys"     "Choerodon"         
 [37] "Megalaspis"         "Gempylus"           "Verulux"           
 [40] "Neopomacentrus"     "Zoramia"            "Butis"             
 [43] "Plectorhinchus"     "Mugil"              "Amblyglyphidodon"  
 [46] "Asterropteryx"      "Fundulus"           "Sphyraena"         
 [49] "Ctenogobiops"       "Microgobius"        "Parupeneus"        
 [52] "Couesius"           "Chaetodipterus"     "Diaphus"           
 [55] "Gymnothorax"        "Upeneus"            "Gobio"             
 [58] "Thalassoma"         "Carassius"          "Hemiglyphidodon"   
 [61] "Gambusia"           "Ptereleotris"       "Hyporhamphus"      
 [64] "Oplopomus"          "Naso"               "Cheiloprion"       
 [67] "Euthynnus"          "Atherinomorus"      "Arothron"          
 [70] "Morone"             "Herklotsichthys"    "Centropyge"        
 [73] "Eugerres"           "Centrobranchus"     "Scomberomorus"     
 [76] "Sardinops"          "Stenatherina"       "Taractes"          
 [79] "Chaetodon"          "Brevoortia"         "Sufflamen"         
 [82] "Plectropomus"       "Koumansetta"        "Sander"            
 [85] "Balistapus"         "Sargocentron"       "Ecsenius"          
 [88] "Ostorhinchus"       "Engraulis"          "Cephalopholis"     
 [91] "Pervagor"           "Eviota"             "Strongylura"       
 [94] "Pseudochromis"      "Leptoscarus"        "Chlorurus"         
 [97] "Macolor"            "Grammatorcynus"     "Uropterygius"      
[100] "Cirripectes"        "Vinciguerria"       "Petroscirtes"      
[103] "Neoniphon"          "Callionymus"        "Chanos"            
[106] "Cypselurus"         "Pseudorca"          "Pristicon"         
[109] "Hemigymnus"         "Amblygaster"        "Erythrocles"       
[112] "Chrysiptera"        "Enchelycore"        "Pristiapogon"      
[115] "Gazza"              "Coptodon"           "Mugilogobius"      
[118] "Atule"              "Cyprinodon"         "Lagodon"           
[121] "Lampadena"          "Synodus"            "Amblygobius"       
[124] "Cercamia"           "Pomacanthus"        "Sueviota"          
[127] "Cabillus"           "Pomadasys"          "Enneapterygius"    
[130] "Cymolutes"          "Cyclothone"         "Conger"            
[133] "Photopectoralis"    "Cryptocentrus"      "Gobiosoma"         
[136] "Platax"             "Thymallus"          "Carangoides"       
[139] "Cyprinella"         "Monodactylus"       "Salarias"          
[142] "Scarus"             "Stenella"           "Gnathodentex"      
[145] "Sphaeramia"         "Barbatula"          "Epinephelus"       
[148] "Campostoma"         "Cheilodipterus"     "Aprion"            
[151] "Moringua"           "Cymbacephalus"      "Halichoeres"       
[154] "Toxotes"            "Melichthys"         "Stolephorus"       
[157] "Plectroglyphidodon" "Parexocoetus"       "Leiuranus"         
[160] "Ceratoscopelus"     "Aurigequula"        "Auxis"             
[163] "Zebrasoma"          "Oxyurichthys"       "Ophiocara"         
[166] "Fibramia"           "Chaetodontoplus"    "Gnathanodon"       
[169] "Siphamia"           "Valenciennea"       "Pseudodax"         
[172] "Novaculichthys"     "Diproctacanthus"    "Apogonichthyoides" 
[175] "Xanthichthys"       "Dischistodus"       "Parioglossus"      
[178] "Catostomus"         "Apogon"             "Sebastapistes"     
[181] "Rhinecanthus"       "Caracanthus"        "Rudarius"          
[184] "Lubbockichthys"     "Hipposcarus"        "Diodon"            
[187] "Scomberoides"       "Bregmaceros"        "Favonigobius"      
[190] "Saurida"            "Diplogrammus"       "Nectamia"          
[193] "Gobiopsis"          "Cheilinus"          "Scorpaenopsis"     
[196] "Vanderhorstia"      "Calotomus"          "Cantherhines"      
[199] "Abudefduf"          "Gunnellichthys"     "Fistularia"        
[202] "Pleurosicya"        "Zenarchopterus"     "Echeneis"          
[205] "Trichonotus"        "Cociella"           "Acreichthys"       
[208] "Rhabdamia"          "Gnatholepis"        "Stegastes"         
[211] "Blenniella"         "Coryphaena"         "Cirrhilabrus"      
[214] "Gibbonsia"          "Exyrias"            "Nannosalarias"     
[217] "Amblyeleotris"      "Stethojulis"        "Symphorichthys"    
[220] "Albula"             "Acentrogobius"      "Salmo"             
[223] "Fowleria"           "Gomphosus"          "Schindleria"       
[226] "Canthigaster"       "Chromis"            "Bostrychus"        
[229] "Elagatis"           "Oxycheilinus"       "Diagramma"         
[232] "Trachinotus"        "Novaculoides"       "Pseudogramma"      
[235] "Macrodontogobius"   "Aseraggodes"        "Apolemichthys"     
[238] "Scorpaenodes"       "Fusigobius"         "Foa"               
[241] "Aluterus"           "Scolopsis"          "Antennatus"        
[244] "Megalops"           "Ariosoma"           "Enchelynassa"      
[247] "Coris"              "Labroides"          "Iso"               
[250] "Parapercis"         "Pseudocheilinus"    "Heteropriacanthus" 
[253] "Cirrhitus"          "Redigobius"         "Carapus"           
[256] "Plectrypops"        "Amblycirrhitus"     "Trimma"            
[259] "Dascyllus"         
  [1] "Cheilopogon"        "Thunnus"            "Decapterus"        
  [4] "Katsuwonus"         "Oncorhynchus"       NA                  
  [7] "Encrasicholina"     "Lethrinus"          "Selar"             
 [10] "Kyphosus"           "Ctenochaetus"       "Hypoatherina"      
 [13] "Spratelloides"      "Gerres"             "Acanthurus"        
 [16] "Oxyporhamphus"      "Callogobius"        "Caesio"            
 [19] "Myripristis"        "Tylosurus"          "Pterocaesio"       
 [22] "Lutjanus"           "Hemiramphus"        "Pomacentrus"       
 [25] "Siganus"            "Caranx"             "Monotaxis"         
 [28] "Mulloidichthys"     "Choerodon"          "Megalaspis"        
 [31] "Verulux"            "Neopomacentrus"     "Zoramia"           
 [34] "Butis"              "Plectorhinchus"     "Mugil"             
 [37] "Amblyglyphidodon"   "Asterropteryx"      "Bolinichthys"      
 [40] "Sphyraena"          "Ctenogobiops"       "Parupeneus"        
 [43] "Diaphus"            "Gymnothorax"        "Upeneus"           
 [46] "Gobio"              "Thalassoma"         "Hemiglyphidodon"   
 [49] "Gambusia"           "Hyporhamphus"       "Oplopomus"         
 [52] "Naso"               "Cheiloprion"        "Euthynnus"         
 [55] "Atherinomorus"      "Arothron"           "Herklotsichthys"   
 [58] "Centropyge"         "Scomberomorus"      "Sardinops"         
 [61] "Stenatherina"       "Chaetodon"          "Sufflamen"         
 [64] "Plectropomus"       "Koumansetta"        "Sander"            
 [67] "Balistapus"         "Sargocentron"       "Ecsenius"          
 [70] "Ostorhinchus"       "Cephalopholis"      "Pervagor"          
 [73] "Eviota"             "Strongylura"        "Myctophum"         
 [76] "Pseudochromis"      "Leptoscarus"        "Chlorurus"         
 [79] "Macolor"            "Grammatorcynus"     "Uropterygius"      
 [82] "Petroscirtes"       "Neoniphon"          "Callionymus"       
 [85] "Chanos"             "Pristicon"          "Hemigymnus"        
 [88] "Amblygaster"        "Erythrocles"        "Chrysiptera"       
 [91] "Carassius"          "Enchelycore"        "Pristiapogon"      
 [94] "Gazza"              "Mugilogobius"       "Atule"             
 [97] "Cyprinodon"         "Lagodon"            "Synodus"           
[100] "Amblygobius"        "Cercamia"           "Pomacanthus"       
[103] "Sueviota"           "Engraulis"          "Cabillus"          
[106] "Pomadasys"          "Enneapterygius"     "Cymolutes"         
[109] "Conger"             "Photopectoralis"    "Cryptocentrus"     
[112] "Gobiosoma"          "Eugerres"           "Platax"            
[115] "Carangoides"        "Monodactylus"       "Salarias"          
[118] "Scarus"             "Gnathodentex"       "Sphaeramia"        
[121] "Epinephelus"        "Campostoma"         "Cheilodipterus"    
[124] "Aprion"             "Moringua"           "Cymbacephalus"     
[127] "Halichoeres"        "Toxotes"            "Melichthys"        
[130] "Stolephorus"        "Plectroglyphidodon" "Parexocoetus"      
[133] "Leiuranus"          "Aurigequula"        "Auxis"             
[136] "Zebrasoma"          "Oxyurichthys"       "Ophiocara"         
[139] "Fibramia"           "Chaetodontoplus"    "Gnathanodon"       
[142] "Fundulus"           "Siphamia"           "Valenciennea"      
[145] "Pseudodax"          "Novaculichthys"     "Diproctacanthus"   
[148] "Apogonichthyoides"  "Dischistodus"       "Parioglossus"      
[151] "Apogon"             "Sebastapistes"      "Rhinecanthus"      
[154] "Caracanthus"        "Rudarius"           "Lubbockichthys"    
[157] "Hipposcarus"        "Diodon"             "Scomberoides"      
[160] "Bregmaceros"        "Favonigobius"       "Saurida"           
[163] "Diplogrammus"       "Nectamia"           "Gobiopsis"         
[166] "Cheilinus"          "Scorpaenopsis"      "Vanderhorstia"     
[169] "Chaetodipterus"     "Calotomus"          "Cantherhines"      
[172] "Abudefduf"          "Gunnellichthys"     "Fistularia"        
[175] "Microgobius"        "Ptereleotris"       "Pleurosicya"       
[178] "Zenarchopterus"     "Echeneis"           "Trichonotus"       
[181] "Cociella"           "Acreichthys"        "Brevoortia"        
[184] "Rhabdamia"          "Gnatholepis"        "Stegastes"         
[187] "Blenniella"         "Cirrhilabrus"       "Cirripectes"       
[190] "Exyrias"            "Nannosalarias"      "Amblyeleotris"     
[193] "Stethojulis"        "Symphorichthys"     "Albula"            
[196] "Acentrogobius"      "Salmo"              "Fowleria"          
[199] "Gomphosus"          "Schindleria"        "Canthigaster"      
[202] "Chromis"            "Bostrychus"         "Elagatis"          
[205] "Oxycheilinus"       "Diagramma"          "Trachinotus"       
[208] "Novaculoides"       "Pseudogramma"       "Macrodontogobius"  
[211] "Aseraggodes"        "Apolemichthys"      "Scorpaenodes"      
[214] "Fusigobius"         "Foa"                "Aluterus"          
[217] "Scolopsis"          "Antennatus"         "Megalops"          
[220] "Ariosoma"           "Enchelynassa"       "Coris"             
[223] "Labroides"          "Iso"                "Parapercis"        
[226] "Pseudocheilinus"    "Heteropriacanthus"  "Redigobius"        
[229] "Carapus"            "Trimma"             "Dascyllus"         
 [1] "Cheilopogon"        "Thunnus"            "Myctophum"         
 [4] "Exocoetus"          "Decapterus"         "Katsuwonus"        
 [7] "Oncorhynchus"       NA                   "Prognichthys"      
[10] "Selar"              "Kyphosus"           "Bolinichthys"      
[13] "Cubiceps"           "Symbolophorus"      "Oxyporhamphus"     
[16] "Myripristis"        "Tylosurus"          "Hygophum"          
[19] "Siganus"            "Mulloidichthys"     "Gempylus"          
[22] "Mugil"              "Fundulus"           "Sphyraena"         
[25] "Acanthurus"         "Microgobius"        "Parupeneus"        
[28] "Couesius"           "Chaetodipterus"     "Gobio"             
[31] "Carassius"          "Gambusia"           "Ptereleotris"      
[34] "Naso"               "Euthynnus"          "Morone"            
[37] "Eugerres"           "Centrobranchus"     "Caranx"            
[40] "Taractes"           "Brevoortia"         "Engraulis"         
[43] "Thalassoma"         "Chlorurus"          "Cirripectes"       
[46] "Vinciguerria"       "Callionymus"        "Diaphus"           
[49] "Hemiramphus"        "Cypselurus"         "Pseudorca"         
[52] "Amblygaster"        "Coptodon"           "Lagodon"           
[55] "Lampadena"          "Cyclothone"         "Thymallus"         
[58] "Cyprinella"         "Stenella"           "Uropterygius"      
[61] "Barbatula"          "Lutjanus"           "Scarus"            
[64] "Ceratoscopelus"     "Xanthichthys"       "Catostomus"        
[67] "Gobiosoma"          "Coryphaena"         "Gibbonsia"         
[70] "Gomphosus"          "Canthigaster"       "Chromis"           
[73] "Sufflamen"          "Ctenochaetus"       "Stegastes"         
[76] "Centropyge"         "Enchelynassa"       "Iso"               
[79] "Plectroglyphidodon" "Pseudogramma"       "Cirrhitus"         
[82] "Plectrypops"        "Amblycirrhitus"    

Species counts of physeq_mar_std object (sf)

  [1] NA                                                     
  [2] "Myctophum lychnobium"                                 
  [3] "Exocoetus volitans"                                   
  [4] "Decapterus macarellus"                                
  [5] "Katsuwonus pelamis"                                   
  [6] "Oncorhynchus tshawytscha"                             
  [7] "Prognichthys sealei"                                  
  [8] "Lethrinus obsoletus"                                  
  [9] "Selar crumenophthalmus"                               
 [10] "Ctenochaetus striatus"                                
 [11] "Hypoatherina celebesensis"                            
 [12] "Spratelloides delicatulus"                            
 [13] "Gerres erythrourus"                                   
 [14] "Symbolophorus evermanni"                              
 [15] "Acanthurus lineatus"                                  
 [16] "Oxyporhamphus micropterus"                            
 [17] "Callogobius sp. 'misuji-haze'"                        
 [18] "Caesio cuning"                                        
 [19] "Tylosurus acus"                                       
 [20] "Pterocaesio tile"                                     
 [21] "Cheilopogon atrisignis"                               
 [22] "Hemiramphus far"                                      
 [23] "Hygophum sp. CBM:ZF:14740"                            
 [24] "Pomacentrus burroughi"                                
 [25] "Monotaxis grandoculis"                                
 [26] "Mulloidichthys flavolineatus"                         
 [27] "Choerodon anchorago"                                  
 [28] "Megalaspis cordyla"                                   
 [29] "Gempylus serpens"                                     
 [30] "Verulux cypselurus"                                   
 [31] "Neopomacentrus nemurus"                               
 [32] "Zoramia viridiventer"                                 
 [33] "Butis butis"                                          
 [34] "Caesio caerulaurea"                                   
 [35] "Plectorhinchus chaetodonoides"                        
 [36] "Mugil cephalus"                                       
 [37] "Asterropteryx semipunctata"                           
 [38] "Bolinichthys longipes"                                
 [39] "Fundulus zebrinus"                                    
 [40] "Acanthurus triostegus"                                
 [41] "Microgobius thalassinus"                              
 [42] "Lethrinus harak"                                      
 [43] "Couesius plumbeus"                                    
 [44] "Chaetodipterus faber"                                 
 [45] "Cheilopogon spilonotopterus"                          
 [46] "Gymnothorax australicola"                             
 [47] "Myripristis greenfieldi"                              
 [48] "Upeneus sulphureus"                                   
 [49] "Gobio gobio"                                          
 [50] "Thalassoma amblycephalum"                             
 [51] "Myripristis violacea"                                 
 [52] "Hemiglyphidodon plagiometopon"                        
 [53] "Myctophum brachygnathum"                              
 [54] "Plectorhinchus schotaf"                               
 [55] "Acanthurus nigricauda"                                
 [56] "Encrasicholina heteroloba"                            
 [57] "Ptereleotris heteroptera"                             
 [58] "Myripristis vittata"                                  
 [59] "Oplopomus oplopomus"                                  
 [60] "Cheiloprion labiatus"                                 
 [61] "Euthynnus affinis"                                    
 [62] "Atherinomorus sp. OCNSW33"                            
 [63] "Morone americana"                                     
 [64] "Lutjanus bohar"                                       
 [65] "Decapterus muroadsi"                                  
 [66] "Herklotsichthys quadrimaculatus"                      
 [67] "Hyporhamphus yuri"                                    
 [68] "Eugerres plumieri"                                    
 [69] "Plectorhinchus lineatus"                              
 [70] "Naso lituratus"                                       
 [71] "Parupeneus barberinus"                                
 [72] "Centrobranchus andreae"                               
 [73] "Scomberomorus sinensis"                               
 [74] "Siganus argenteus"                                    
 [75] "Gymnothorax chilospilus"                              
 [76] "Caranx papuensis"                                     
 [77] "Parupeneus indicus"                                   
 [78] "Myripristis adusta"                                   
 [79] "Stenatherina panatela"                                
 [80] "Taractes rubescens"                                   
 [81] "Brevoortia tyrannus"                                  
 [82] "Plectropomus leopardus"                               
 [83] "Koumansetta hectori"                                  
 [84] "Ctenochaetus binotatus"                               
 [85] "Sander vitreus"                                       
 [86] "Balistapus undulatus"                                 
 [87] "Naso unicornis"                                       
 [88] "Zoramia leptacantha"                                  
 [89] "Ecsenius yaeyamaensis"                                
 [90] "Gymnothorax fimbriatus"                               
 [91] "Engraulis mordax"                                     
 [92] "Cephalopholis urodeta"                                
 [93] "Lutjanus fulvus"                                      
 [94] "Pervagor nigrolineatus"                               
 [95] "Eviota bifasciata"                                    
 [96] "Strongylura incisa"                                   
 [97] "Sphyraena obtusata"                                   
 [98] "Eviota shimadai"                                      
 [99] "Myctophum sp. FLMOO_1333"                             
[100] "Pseudochromis tapeinosoma"                            
[101] "Leptoscarus vaigienis"                                
[102] "Lethrinus erythracanthus"                             
[103] "Siganus doliatus"                                     
[104] "Chlorurus sordidus"                                   
[105] "Macolor macularis"                                    
[106] "Gymnothorax buroensis"                                
[107] "Grammatorcynus bilineatus"                            
[108] "Uropterygius alboguttatus"                            
[109] "Sargocentron tiere"                                   
[110] "Vinciguerria sp. CBM:ZF:14736"                        
[111] "Neoniphon sammara"                                    
[112] "Callionymus marquesensis"                             
[113] "Chaetodon ephippium"                                  
[114] "Diaphus splendidus"                                   
[115] "Naso vlamingii"                                       
[116] "Callionymus enneactis"                                
[117] "Hemiramphus convexus"                                 
[118] "Chanos chanos"                                        
[119] "Cypselurus angusticeps"                               
[120] "Pseudorca crassidens"                                 
[121] "Pristicon rhodopterus"                                
[122] "Hemigymnus melapterus"                                
[123] "Amblygaster sirm"                                     
[124] "Erythrocles schlegelii"                               
[125] "Chaetodon ulietensis"                                 
[126] "Chrysiptera cyanea"                                   
[127] "Enchelycore bayeri"                                   
[128] "Ctenogobiops feroculus"                               
[129] "Pomacentrus pavo"                                     
[130] "Eviota punctulata"                                    
[131] "Pterocaesio digramma"                                 
[132] "Pristiapogon exostigma"                               
[133] "Lethrinus reticulatus"                                
[134] "Chaetodon auriga"                                     
[135] "Lethrinus atkinsoni"                                  
[136] "Gazza achlamys"                                       
[137] "Coptodon zillii"                                      
[138] "Mugilogobius sp. 'tanuki-haze'"                       
[139] "Atule mate"                                           
[140] "Lagodon rhomboides"                                   
[141] "Lampadena luminosa"                                   
[142] "Synodus dermatogenys"                                 
[143] "Siganus spinus"                                       
[144] "Amblygobius decussatus"                               
[145] "Cercamia eremia"                                      
[146] "Pomacanthus xanthometopon"                            
[147] "Plectropomus areolatus"                               
[148] "Sueviota sp. MOOP_2911"                               
[149] "Upeneus guttatus"                                     
[150] "Thalassoma quinquevittatum"                           
[151] "Gymnothorax thyrsoideus"                              
[152] "Pomadasys sp. CBM:ZF:18112"                           
[153] "Enneapterygius tutuilae"                              
[154] "Cymolutes praetextatus"                               
[155] "Cyclothone alba"                                      
[156] "Conger cinereus"                                      
[157] "Photopectoralis bindus"                               
[158] "Cryptocentrus caeruleomaculatus"                      
[159] "Gymnothorax zonipectis"                               
[160] "Myripristis pralinia"                                 
[161] "Amblygobius nocturnus"                                
[162] "Gobiosoma ginsburgi"                                  
[163] "Gymnothorax margaritophorus"                          
[164] "Myripristis chryseres"                                
[165] "Platax orbicularis"                                   
[166] "Thymallus arcticus"                                   
[167] "Carangoides plagiotaenia"                             
[168] "Cyprinella spiloptera"                                
[169] "Monodactylus argenteus"                               
[170] "Lethrinus olivaceus"                                  
[171] "Salarias sinuosus"                                    
[172] "Scarus psittacus"                                     
[173] "Stenella attenuata"                                   
[174] "Gnathodentex aureolineatus"                           
[175] "Sphaeramia orbicularis"                               
[176] "Amblygobius phalaena"                                 
[177] "Callionymus simplicicornis"                           
[178] "Pomacentrus vaiuli"                                   
[179] "Uropterygius micropterus"                             
[180] "Gerres longirostris"                                  
[181] "Tylosurus crocodilus"                                 
[182] "Barbatula barbatula"                                  
[183] "Chrysiptera glauca"                                   
[184] "Epinephelus polyphekadion"                            
[185] "Salarias segmentatus"                                 
[186] "Mugil curema"                                         
[187] "Lethrinus lentjan"                                    
[188] "Gymnothorax pindae"                                   
[189] "Aprion virescens"                                     
[190] "Moringua javanica"                                    
[191] "Lutjanus monostigma"                                  
[192] "Pterocaesio tessellata"                               
[193] "Cymbacephalus beauforti"                              
[194] "Halichoeres trimaculatus"                             
[195] "Toxotes jaculatrix"                                   
[196] "Stolephorus teguhi"                                   
[197] "Scarus schlegeli"                                     
[198] "Plectroglyphidodon lacrymatus"                        
[199] "Eviota prasina"                                       
[200] "Parexocoetus mento"                                   
[201] "Leiuranus semicinctus"                                
[202] "Eviota masudai"                                       
[203] "Diaphus sp. CBM DNA No. 2014-626"                     
[204] "Aurigequula fasciata"                                 
[205] "Auxis thazard"                                        
[206] "Chaetodon citrinellus"                                
[207] "Caranx ignobilis"                                     
[208] "Ophiocara porocephala"                                
[209] "Gymnothorax richardsonii"                             
[210] "Fibramia thermalis"                                   
[211] "Chaetodontoplus poliourus"                            
[212] "Scarus niger"                                         
[213] "Acanthurus mata"                                      
[214] "Gnathanodon speciosus"                                
[215] "Gymnothorax flavimarginatus"                          
[216] "Sargocentron diadema"                                 
[217] "Fundulus grandis"                                     
[218] "Halichoeres melanurus"                                
[219] "Sargocentron punctatissimum"                          
[220] "Siphamia tubifer"                                     
[221] "Valenciennea sexguttata"                              
[222] "Pseudochromis marshallensis"                          
[223] "Thalassoma hardwicke"                                 
[224] "Petroscirtes mitratus"                                
[225] "Scarus dimidiatus"                                    
[226] "Pseudodax moluccanus"                                 
[227] "Gerres oblongus"                                      
[228] "Naso brachycentron"                                   
[229] "Novaculichthys taeniourus"                            
[230] "Chaetodon semeion"                                    
[231] "Diproctacanthus xanthurus"                            
[232] "Apogonichthyoides melas"                              
[233] "Epinephelus merra"                                    
[234] "Xanthichthys caeruleolineatus"                        
[235] "Parioglossus palustris"                               
[236] "Catostomus catostomus"                                
[237] "Lutjanus gibbus"                                      
[238] "Apogon hyalosoma"                                     
[239] "Stenella longirostris"                                
[240] "Sebastapistes sp. OCF-P20130923-2"                    
[241] "Eviota guttata"                                       
[242] "Rhinecanthus verrucosus"                              
[243] "Caracanthus unipinna"                                 
[244] "Cryptocentrus melanopus"                              
[245] "Rudarius ercodes"                                     
[246] "Acanthurus nigrofuscus"                               
[247] "Acanthurus olivaceus"                                 
[248] "Fibramia amboinensis"                                 
[249] "Lubbockichthys sp. MOOP_6973"                         
[250] "Enchelycore kamara"                                   
[251] "Hipposcarus longiceps"                                
[252] "Atherinomorus cf. regina FRLM:40035"                  
[253] "Chaetodon octofasciatus"                              
[254] "Favonigobius sp. OCF-P3775"                           
[255] "Lethrinus haematopterus"                              
[256] "Rhinecanthus aculeatus"                               
[257] "Saurida gracilis"                                     
[258] "Pristiapogon kallopterus"                             
[259] "Diplogrammus xenicus"                                 
[260] "Cephalopholis argus"                                  
[261] "Lethrinus xanthochilus"                               
[262] "Epinephelus hexagonatus"                              
[263] "Nectamia fusca"                                       
[264] "Chlorurus bleekeri"                                   
[265] "Chrysiptera oxycephala"                               
[266] "Gobiopsis arenaria"                                   
[267] "Cheilinus undulatus"                                  
[268] "Scorpaenopsis possi"                                  
[269] "Myripristis hexagona"                                 
[270] "Halichoeres leucurus"                                 
[271] "Calotomus spinidens"                                  
[272] "Cantherhines dumerilii"                               
[273] "Abudefduf septemfasciatus"                            
[274] "Diaphus bertelseni"                                   
[275] "Neoniphon aurolineatus"                               
[276] "Gunnellichthys monostigma"                            
[277] "Zebrasoma velifer"                                    
[278] "Fistularia commersonii"                               
[279] "Scomberoides lysan"                                   
[280] "Ptereleotris evides"                                  
[281] "Scarus rubroviolaceus"                                
[282] "Saurida nebulosa"                                     
[283] "Sebastapistes strongia"                               
[284] "Pleurosicya bilobata"                                 
[285] "Zenarchopterus buffonis"                              
[286] "Cociella punctata"                                    
[287] "Halichoeres hortulanus"                               
[288] "Atherinomorus lacunosus"                              
[289] "Plectroglyphidodon dickii"                            
[290] "Plectroglyphidodon leucozonus"                        
[291] "Callogobius maculipinnis"                             
[292] "Rhabdamia spilota"                                    
[293] "Gnatholepis anjerensis"                               
[294] "Stegastes nigricans"                                  
[295] "Sargocentron microstoma"                              
[296] "Neoniphon opercularis"                                
[297] "Blenniella sp. MOH-040"                               
[298] "Coryphaena hippurus"                                  
[299] "Salarias ceramensis"                                  
[300] "Epinephelus tauvina"                                  
[301] "Cheilodipterus quinquelineatus"                       
[302] "Cirripectes imitator"                                 
[303] "Neoniphon argenteus"                                  
[304] "Dischistodus melanotus"                               
[305] "Gibbonsia montereyensis"                              
[306] "Exyrias belissimus"                                   
[307] "Nannosalarias nativitatis"                            
[308] "Amblyeleotris steinitzi"                              
[309] "Stethojulis strigiventer"                             
[310] "Symphorichthys spilurus"                              
[311] "Nectamia savayensis"                                  
[312] "Albula glossodonta"                                   
[313] "Diodon liturosus"                                     
[314] "Acentrogobius janthinopterus"                         
[315] "Salmo salar"                                          
[316] "Fowleria variegata"                                   
[317] "Gomphosus varius"                                     
[318] "Schindleria praematura"                               
[319] "Fowleria isostigma"                                   
[320] "Chromis vanderbilti"                                  
[321] "Lutjanus kasmira"                                     
[322] "Bostrychus sinensis"                                  
[323] "Amblygaster leiogaster"                               
[324] "Sufflamen bursa"                                      
[325] "Elagatis bipinnulata"                                 
[326] "Scarus forsteni"                                      
[327] "Oxycheilinus unifasciatus"                            
[328] "Trachinotus blochii"                                  
[329] "Stethojulis bandanensis"                              
[330] "Stegastes lividus"                                    
[331] "Novaculoides macrolepidotus"                          
[332] "Pseudogramma polyacantha"                             
[333] "Scarus ghobban"                                       
[334] "Macrodontogobius wilburi"                             
[335] "Aseraggodes cheni"                                    
[336] "Cryptocentrus nigrocellatus"                          
[337] "Scorpaenodes guamensis"                               
[338] "Fusigobius signipinnis"                               
[339] "Sphyraena putnamae"                                   
[340] "Chromis viridis"                                      
[341] "Foa fo"                                               
[342] "Gnatholepis cauerensis"                               
[343] "Sphyraena iburiensis"                                 
[344] "Halichoeres nebulosus"                                
[345] "Pseudochromis fuscus"                                 
[346] "Aluterus scriptus"                                    
[347] "Scolopsis bilineata"                                  
[348] "Sargocentron spiniferum"                              
[349] "Antennatus dorehensis"                                
[350] "Megalops cyprinoides"                                 
[351] "Sphaeramia nematoptera"                               
[352] "Ctenochaetus hawaiiensis"                             
[353] "Scarus rivulatus"                                     
[354] "Chlorurus japanensis"                                 
[355] "Valenciennea longipinnis"                             
[356] "Diaphus brachycephalus"                               
[357] "Chromis lepidolepis"                                  
[358] "Lutjanus fulviflamma"                                 
[359] "Cymolutes torquatus"                                  
[360] "Oncorhynchus kisutch"                                 
[361] "Epinephelus fuscoguttatus x Epinephelus polyphekadion"
[362] "Upeneus tragula"                                      
[363] "Ariosoma scheelei"                                    
[364] "Stethojulis trilineata"                               
[365] "Enchelynassa canina"                                  
[366] "Coris batuensis"                                      
[367] "Labroides dimidiatus"                                 
[368] "Iso flosmaris"                                        
[369] "Eviota latifasciata"                                  
[370] "Moringua edwardsi"                                    
[371] "Parapercis cylindrica"                                
[372] "Plectroglyphidodon imparipennis"                      
[373] "Exyrias puntang"                                      
[374] "Parupeneus cyclostomus"                               
[375] "Centropyge tibicen"                                   
[376] "Pseudogramma brederi"                                 
[377] "Cabillus tongarevae"                                  
[378] "Pseudocheilinus evanidus"                             
[379] "Heteropriacanthus cruentatus"                         
[380] "Cirrhitus pinnulatus"                                 
[381] "Acanthurus leucopareius"                              
[382] "Redigobius bikolanus"                                 
[383] "Carapus mourlani"                                     
[384] "Plectrypops lima"                                     
[385] "Fundulus heteroclitus"                                
[386] "Amblycirrhitus bimacula"                              
[387] "Trimma striatum"                                      
[388] "Dascyllus trimaculatus"                               
  [1] NA                                                     
  [2] "Decapterus macarellus"                                
  [3] "Katsuwonus pelamis"                                   
  [4] "Oncorhynchus tshawytscha"                             
  [5] "Lethrinus obsoletus"                                  
  [6] "Selar crumenophthalmus"                               
  [7] "Ctenochaetus striatus"                                
  [8] "Hypoatherina celebesensis"                            
  [9] "Spratelloides delicatulus"                            
 [10] "Gerres erythrourus"                                   
 [11] "Acanthurus lineatus"                                  
 [12] "Oxyporhamphus micropterus"                            
 [13] "Callogobius sp. 'misuji-haze'"                        
 [14] "Caesio cuning"                                        
 [15] "Tylosurus acus"                                       
 [16] "Pterocaesio tile"                                     
 [17] "Cheilopogon atrisignis"                               
 [18] "Hemiramphus far"                                      
 [19] "Pomacentrus burroughi"                                
 [20] "Monotaxis grandoculis"                                
 [21] "Mulloidichthys flavolineatus"                         
 [22] "Choerodon anchorago"                                  
 [23] "Megalaspis cordyla"                                   
 [24] "Verulux cypselurus"                                   
 [25] "Neopomacentrus nemurus"                               
 [26] "Zoramia viridiventer"                                 
 [27] "Butis butis"                                          
 [28] "Caesio caerulaurea"                                   
 [29] "Plectorhinchus chaetodonoides"                        
 [30] "Mugil cephalus"                                       
 [31] "Asterropteryx semipunctata"                           
 [32] "Bolinichthys longipes"                                
 [33] "Acanthurus triostegus"                                
 [34] "Lethrinus harak"                                      
 [35] "Gymnothorax australicola"                             
 [36] "Myripristis greenfieldi"                              
 [37] "Upeneus sulphureus"                                   
 [38] "Gobio gobio"                                          
 [39] "Thalassoma amblycephalum"                             
 [40] "Myripristis violacea"                                 
 [41] "Hemiglyphidodon plagiometopon"                        
 [42] "Plectorhinchus schotaf"                               
 [43] "Acanthurus nigricauda"                                
 [44] "Encrasicholina heteroloba"                            
 [45] "Oplopomus oplopomus"                                  
 [46] "Cheiloprion labiatus"                                 
 [47] "Euthynnus affinis"                                    
 [48] "Atherinomorus sp. OCNSW33"                            
 [49] "Lutjanus bohar"                                       
 [50] "Herklotsichthys quadrimaculatus"                      
 [51] "Hyporhamphus yuri"                                    
 [52] "Plectorhinchus lineatus"                              
 [53] "Naso lituratus"                                       
 [54] "Parupeneus barberinus"                                
 [55] "Scomberomorus sinensis"                               
 [56] "Siganus argenteus"                                    
 [57] "Gymnothorax chilospilus"                              
 [58] "Caranx papuensis"                                     
 [59] "Parupeneus indicus"                                   
 [60] "Myripristis adusta"                                   
 [61] "Stenatherina panatela"                                
 [62] "Plectropomus leopardus"                               
 [63] "Koumansetta hectori"                                  
 [64] "Ctenochaetus binotatus"                               
 [65] "Sander vitreus"                                       
 [66] "Balistapus undulatus"                                 
 [67] "Naso unicornis"                                       
 [68] "Zoramia leptacantha"                                  
 [69] "Ecsenius yaeyamaensis"                                
 [70] "Gymnothorax fimbriatus"                               
 [71] "Cephalopholis urodeta"                                
 [72] "Lutjanus fulvus"                                      
 [73] "Pervagor nigrolineatus"                               
 [74] "Eviota bifasciata"                                    
 [75] "Strongylura incisa"                                   
 [76] "Sphyraena obtusata"                                   
 [77] "Eviota shimadai"                                      
 [78] "Myctophum sp. FLMOO_1333"                             
 [79] "Pseudochromis tapeinosoma"                            
 [80] "Leptoscarus vaigienis"                                
 [81] "Lethrinus erythracanthus"                             
 [82] "Siganus doliatus"                                     
 [83] "Chlorurus sordidus"                                   
 [84] "Macolor macularis"                                    
 [85] "Gymnothorax buroensis"                                
 [86] "Grammatorcynus bilineatus"                            
 [87] "Uropterygius alboguttatus"                            
 [88] "Sargocentron tiere"                                   
 [89] "Neoniphon sammara"                                    
 [90] "Chaetodon ephippium"                                  
 [91] "Naso vlamingii"                                       
 [92] "Callionymus enneactis"                                
 [93] "Hemiramphus convexus"                                 
 [94] "Chanos chanos"                                        
 [95] "Pristicon rhodopterus"                                
 [96] "Hemigymnus melapterus"                                
 [97] "Amblygaster sirm"                                     
 [98] "Erythrocles schlegelii"                               
 [99] "Chaetodon ulietensis"                                 
[100] "Chrysiptera cyanea"                                   
[101] "Enchelycore bayeri"                                   
[102] "Ctenogobiops feroculus"                               
[103] "Pomacentrus pavo"                                     
[104] "Eviota punctulata"                                    
[105] "Pterocaesio digramma"                                 
[106] "Pristiapogon exostigma"                               
[107] "Lethrinus reticulatus"                                
[108] "Chaetodon auriga"                                     
[109] "Lethrinus atkinsoni"                                  
[110] "Gazza achlamys"                                       
[111] "Mugilogobius sp. 'tanuki-haze'"                       
[112] "Atule mate"                                           
[113] "Lagodon rhomboides"                                   
[114] "Synodus dermatogenys"                                 
[115] "Siganus spinus"                                       
[116] "Amblygobius decussatus"                               
[117] "Cercamia eremia"                                      
[118] "Pomacanthus xanthometopon"                            
[119] "Plectropomus areolatus"                               
[120] "Sueviota sp. MOOP_2911"                               
[121] "Upeneus guttatus"                                     
[122] "Thalassoma quinquevittatum"                           
[123] "Gymnothorax thyrsoideus"                              
[124] "Pomadasys sp. CBM:ZF:18112"                           
[125] "Enneapterygius tutuilae"                              
[126] "Cymolutes praetextatus"                               
[127] "Conger cinereus"                                      
[128] "Photopectoralis bindus"                               
[129] "Cryptocentrus caeruleomaculatus"                      
[130] "Gymnothorax zonipectis"                               
[131] "Myripristis pralinia"                                 
[132] "Amblygobius nocturnus"                                
[133] "Gobiosoma ginsburgi"                                  
[134] "Gymnothorax margaritophorus"                          
[135] "Eugerres plumieri"                                    
[136] "Platax orbicularis"                                   
[137] "Carangoides plagiotaenia"                             
[138] "Monodactylus argenteus"                               
[139] "Lethrinus olivaceus"                                  
[140] "Salarias sinuosus"                                    
[141] "Scarus psittacus"                                     
[142] "Gnathodentex aureolineatus"                           
[143] "Sphaeramia orbicularis"                               
[144] "Amblygobius phalaena"                                 
[145] "Callionymus simplicicornis"                           
[146] "Pomacentrus vaiuli"                                   
[147] "Gerres longirostris"                                  
[148] "Tylosurus crocodilus"                                 
[149] "Chrysiptera glauca"                                   
[150] "Epinephelus polyphekadion"                            
[151] "Salarias segmentatus"                                 
[152] "Mugil curema"                                         
[153] "Lethrinus lentjan"                                    
[154] "Gymnothorax pindae"                                   
[155] "Aprion virescens"                                     
[156] "Moringua javanica"                                    
[157] "Lutjanus monostigma"                                  
[158] "Pterocaesio tessellata"                               
[159] "Cymbacephalus beauforti"                              
[160] "Halichoeres trimaculatus"                             
[161] "Toxotes jaculatrix"                                   
[162] "Stolephorus teguhi"                                   
[163] "Scarus schlegeli"                                     
[164] "Plectroglyphidodon lacrymatus"                        
[165] "Eviota prasina"                                       
[166] "Parexocoetus mento"                                   
[167] "Leiuranus semicinctus"                                
[168] "Eviota masudai"                                       
[169] "Diaphus sp. CBM DNA No. 2014-626"                     
[170] "Aurigequula fasciata"                                 
[171] "Auxis thazard"                                        
[172] "Chaetodon citrinellus"                                
[173] "Caranx ignobilis"                                     
[174] "Ophiocara porocephala"                                
[175] "Gymnothorax richardsonii"                             
[176] "Fibramia thermalis"                                   
[177] "Chaetodontoplus poliourus"                            
[178] "Scarus niger"                                         
[179] "Acanthurus mata"                                      
[180] "Gnathanodon speciosus"                                
[181] "Gymnothorax flavimarginatus"                          
[182] "Sargocentron diadema"                                 
[183] "Fundulus grandis"                                     
[184] "Halichoeres melanurus"                                
[185] "Sargocentron punctatissimum"                          
[186] "Siphamia tubifer"                                     
[187] "Valenciennea sexguttata"                              
[188] "Pseudochromis marshallensis"                          
[189] "Thalassoma hardwicke"                                 
[190] "Petroscirtes mitratus"                                
[191] "Scarus dimidiatus"                                    
[192] "Pseudodax moluccanus"                                 
[193] "Gerres oblongus"                                      
[194] "Naso brachycentron"                                   
[195] "Novaculichthys taeniourus"                            
[196] "Chaetodon semeion"                                    
[197] "Diproctacanthus xanthurus"                            
[198] "Apogonichthyoides melas"                              
[199] "Epinephelus merra"                                    
[200] "Parioglossus palustris"                               
[201] "Lutjanus gibbus"                                      
[202] "Apogon hyalosoma"                                     
[203] "Sebastapistes sp. OCF-P20130923-2"                    
[204] "Eviota guttata"                                       
[205] "Rhinecanthus verrucosus"                              
[206] "Caracanthus unipinna"                                 
[207] "Cryptocentrus melanopus"                              
[208] "Rudarius ercodes"                                     
[209] "Acanthurus nigrofuscus"                               
[210] "Acanthurus olivaceus"                                 
[211] "Fibramia amboinensis"                                 
[212] "Lubbockichthys sp. MOOP_6973"                         
[213] "Enchelycore kamara"                                   
[214] "Hipposcarus longiceps"                                
[215] "Atherinomorus cf. regina FRLM:40035"                  
[216] "Chaetodon octofasciatus"                              
[217] "Favonigobius sp. OCF-P3775"                           
[218] "Lethrinus haematopterus"                              
[219] "Rhinecanthus aculeatus"                               
[220] "Saurida gracilis"                                     
[221] "Pristiapogon kallopterus"                             
[222] "Diplogrammus xenicus"                                 
[223] "Cephalopholis argus"                                  
[224] "Lethrinus xanthochilus"                               
[225] "Epinephelus hexagonatus"                              
[226] "Nectamia fusca"                                       
[227] "Chlorurus bleekeri"                                   
[228] "Chrysiptera oxycephala"                               
[229] "Gobiopsis arenaria"                                   
[230] "Cheilinus undulatus"                                  
[231] "Scorpaenopsis possi"                                  
[232] "Myripristis hexagona"                                 
[233] "Chaetodipterus faber"                                 
[234] "Halichoeres leucurus"                                 
[235] "Calotomus spinidens"                                  
[236] "Cantherhines dumerilii"                               
[237] "Abudefduf septemfasciatus"                            
[238] "Diaphus bertelseni"                                   
[239] "Neoniphon aurolineatus"                               
[240] "Gunnellichthys monostigma"                            
[241] "Zebrasoma velifer"                                    
[242] "Fistularia commersonii"                               
[243] "Scomberoides lysan"                                   
[244] "Microgobius thalassinus"                              
[245] "Ptereleotris evides"                                  
[246] "Scarus rubroviolaceus"                                
[247] "Saurida nebulosa"                                     
[248] "Sebastapistes strongia"                               
[249] "Pleurosicya bilobata"                                 
[250] "Zenarchopterus buffonis"                              
[251] "Cociella punctata"                                    
[252] "Halichoeres hortulanus"                               
[253] "Atherinomorus lacunosus"                              
[254] "Plectroglyphidodon dickii"                            
[255] "Brevoortia tyrannus"                                  
[256] "Plectroglyphidodon leucozonus"                        
[257] "Callogobius maculipinnis"                             
[258] "Rhabdamia spilota"                                    
[259] "Gnatholepis anjerensis"                               
[260] "Stegastes nigricans"                                  
[261] "Sargocentron microstoma"                              
[262] "Neoniphon opercularis"                                
[263] "Blenniella sp. MOH-040"                               
[264] "Salarias ceramensis"                                  
[265] "Epinephelus tauvina"                                  
[266] "Cheilodipterus quinquelineatus"                       
[267] "Cirripectes imitator"                                 
[268] "Neoniphon argenteus"                                  
[269] "Dischistodus melanotus"                               
[270] "Exyrias belissimus"                                   
[271] "Nannosalarias nativitatis"                            
[272] "Amblyeleotris steinitzi"                              
[273] "Stethojulis strigiventer"                             
[274] "Symphorichthys spilurus"                              
[275] "Nectamia savayensis"                                  
[276] "Albula glossodonta"                                   
[277] "Diodon liturosus"                                     
[278] "Acentrogobius janthinopterus"                         
[279] "Salmo salar"                                          
[280] "Fowleria variegata"                                   
[281] "Gomphosus varius"                                     
[282] "Schindleria praematura"                               
[283] "Fowleria isostigma"                                   
[284] "Chromis vanderbilti"                                  
[285] "Lutjanus kasmira"                                     
[286] "Bostrychus sinensis"                                  
[287] "Amblygaster leiogaster"                               
[288] "Sufflamen bursa"                                      
[289] "Elagatis bipinnulata"                                 
[290] "Scarus forsteni"                                      
[291] "Oxycheilinus unifasciatus"                            
[292] "Trachinotus blochii"                                  
[293] "Stethojulis bandanensis"                              
[294] "Stegastes lividus"                                    
[295] "Novaculoides macrolepidotus"                          
[296] "Pseudogramma polyacantha"                             
[297] "Scarus ghobban"                                       
[298] "Macrodontogobius wilburi"                             
[299] "Aseraggodes cheni"                                    
[300] "Cryptocentrus nigrocellatus"                          
[301] "Scorpaenodes guamensis"                               
[302] "Fusigobius signipinnis"                               
[303] "Sphyraena putnamae"                                   
[304] "Chromis viridis"                                      
[305] "Foa fo"                                               
[306] "Gnatholepis cauerensis"                               
[307] "Sphyraena iburiensis"                                 
[308] "Halichoeres nebulosus"                                
[309] "Pseudochromis fuscus"                                 
[310] "Aluterus scriptus"                                    
[311] "Scolopsis bilineata"                                  
[312] "Sargocentron spiniferum"                              
[313] "Antennatus dorehensis"                                
[314] "Megalops cyprinoides"                                 
[315] "Sphaeramia nematoptera"                               
[316] "Ctenochaetus hawaiiensis"                             
[317] "Scarus rivulatus"                                     
[318] "Chlorurus japanensis"                                 
[319] "Valenciennea longipinnis"                             
[320] "Chromis lepidolepis"                                  
[321] "Lutjanus fulviflamma"                                 
[322] "Cymolutes torquatus"                                  
[323] "Oncorhynchus kisutch"                                 
[324] "Epinephelus fuscoguttatus x Epinephelus polyphekadion"
[325] "Upeneus tragula"                                      
[326] "Ariosoma scheelei"                                    
[327] "Stethojulis trilineata"                               
[328] "Enchelynassa canina"                                  
[329] "Coris batuensis"                                      
[330] "Labroides dimidiatus"                                 
[331] "Iso flosmaris"                                        
[332] "Eviota latifasciata"                                  
[333] "Moringua edwardsi"                                    
[334] "Parapercis cylindrica"                                
[335] "Exyrias puntang"                                      
[336] "Centropyge tibicen"                                   
[337] "Pseudogramma brederi"                                 
[338] "Cabillus tongarevae"                                  
[339] "Pseudocheilinus evanidus"                             
[340] "Heteropriacanthus cruentatus"                         
[341] "Acanthurus leucopareius"                              
[342] "Redigobius bikolanus"                                 
[343] "Carapus mourlani"                                     
[344] "Trimma striatum"                                      
[345] "Dascyllus trimaculatus"                               
 [1] NA                                "Myctophum lychnobium"           
 [3] "Exocoetus volitans"              "Decapterus macarellus"          
 [5] "Katsuwonus pelamis"              "Oncorhynchus tshawytscha"       
 [7] "Prognichthys sealei"             "Selar crumenophthalmus"         
 [9] "Symbolophorus evermanni"         "Oxyporhamphus micropterus"      
[11] "Tylosurus acus"                  "Cheilopogon atrisignis"         
[13] "Hygophum sp. CBM:ZF:14740"       "Mulloidichthys flavolineatus"   
[15] "Gempylus serpens"                "Mugil cephalus"                 
[17] "Fundulus zebrinus"               "Acanthurus triostegus"          
[19] "Microgobius thalassinus"         "Couesius plumbeus"              
[21] "Chaetodipterus faber"            "Cheilopogon spilonotopterus"    
[23] "Gobio gobio"                     "Myctophum brachygnathum"        
[25] "Ptereleotris heteroptera"        "Myripristis vittata"            
[27] "Euthynnus affinis"               "Morone americana"               
[29] "Decapterus muroadsi"             "Eugerres plumieri"              
[31] "Parupeneus barberinus"           "Centrobranchus andreae"         
[33] "Caranx papuensis"                "Taractes rubescens"             
[35] "Brevoortia tyrannus"             "Naso unicornis"                 
[37] "Engraulis mordax"                "Chlorurus sordidus"             
[39] "Vinciguerria sp. CBM:ZF:14736"   "Callionymus marquesensis"       
[41] "Diaphus splendidus"              "Hemiramphus convexus"           
[43] "Cypselurus angusticeps"          "Pseudorca crassidens"           
[45] "Amblygaster sirm"                "Coptodon zillii"                
[47] "Lagodon rhomboides"              "Lampadena luminosa"             
[49] "Cyclothone alba"                 "Myripristis chryseres"          
[51] "Thymallus arcticus"              "Cyprinella spiloptera"          
[53] "Stenella attenuata"              "Uropterygius micropterus"       
[55] "Barbatula barbatula"             "Lutjanus monostigma"            
[57] "Scarus schlegeli"                "Xanthichthys caeruleolineatus"  
[59] "Catostomus catostomus"           "Stenella longirostris"          
[61] "Acanthurus nigrofuscus"          "Gobiosoma ginsburgi"            
[63] "Coryphaena hippurus"             "Gibbonsia montereyensis"        
[65] "Gomphosus varius"                "Chromis vanderbilti"            
[67] "Lutjanus kasmira"                "Sufflamen bursa"                
[69] "Cirripectes imitator"            "Ctenochaetus hawaiiensis"       
[71] "Diaphus brachycephalus"          "Oncorhynchus kisutch"           
[73] "Enchelynassa canina"             "Iso flosmaris"                  
[75] "Plectroglyphidodon imparipennis" "Parupeneus cyclostomus"         
[77] "Pseudogramma brederi"            "Cirrhitus pinnulatus"           
[79] "Plectrypops lima"                "Fundulus heteroclitus"          
[81] "Amblycirrhitus bimacula"        

Top

 [1] "ESV_034098" "ESV_033752" "ESV_041947" "ESV_000975" "ESV_042017"
 [6] "ESV_000044" "ESV_000892" "ESV_027356" "ESV_033648" "ESV_001029"

Top Species

$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 11 taxa and 146 samples ]
sample_data() Sample Data:       [ 146 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 11 taxa by 7 taxonomic ranks ]

$top_taxa
   Near_or_Offshore tax_rank      taxid  abundance   Kingdom   Phylum
1              <NA>        1 ESV_041947 0.05937035 Eukaryota Chordata
2              <NA>        2 ESV_033752 0.03769148 Eukaryota Chordata
3              <NA>        5 ESV_000044 0.02115895 Eukaryota Chordata
4              <NA>        7 ESV_001029 0.01529544 Eukaryota Chordata
5              <NA>        4 ESV_042017 0.02127428 Eukaryota Chordata
6              <NA>       10 ESV_040600 0.01360097 Eukaryota Chordata
7              <NA>        3 ESV_000892 0.02895038 Eukaryota Chordata
8              <NA>        9 ESV_040493 0.01378586 Eukaryota Chordata
9              <NA>        6 ESV_033648 0.01707761 Eukaryota Chordata
10             <NA>        8 ESV_000858 0.01447949 Eukaryota Chordata
         Class           Order        Family          Genus
1  Actinopteri  Myctophiformes   Myctophidae      Myctophum
2  Actinopteri    Beloniformes   Exocoetidae      Exocoetus
3  Actinopteri   Carangiformes    Carangidae     Decapterus
4  Actinopteri   Scombriformes    Scombridae     Katsuwonus
5  Actinopteri    Beloniformes   Exocoetidae   Prognichthys
6  Actinopteri     Spariformes   Lethrinidae      Lethrinus
7  Actinopteri   Carangiformes    Carangidae          Selar
8  Actinopteri  Myctophiformes   Myctophidae  Symbolophorus
9  Actinopteri    Beloniformes Hemiramphidae  Oxyporhamphus
10 Actinopteri Syngnathiformes      Mullidae Mulloidichthys
                        Species
1          Myctophum lychnobium
2            Exocoetus volitans
3         Decapterus macarellus
4            Katsuwonus pelamis
5           Prognichthys sealei
6           Lethrinus obsoletus
7        Selar crumenophthalmus
8       Symbolophorus evermanni
9     Oxyporhamphus micropterus
10 Mulloidichthys flavolineatus

Top Nearshore Species

$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 11 taxa and 58 samples ]
sample_data() Sample Data:       [ 58 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 11 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid  abundance   Kingdom   Phylum       Class
1         1 ESV_040600 0.03423692 Eukaryota Chordata Actinopteri
2         2 ESV_000147 0.03225235 Eukaryota Chordata Actinopteri
3         7 ESV_040410 0.01896210 Eukaryota Chordata Actinopteri
4         5 ESV_039694 0.02044955 Eukaryota Chordata Actinopteri
5         3 ESV_000812 0.02154807 Eukaryota Chordata Actinopteri
6         6 ESV_001422 0.01982506 Eukaryota Chordata Actinopteri
7         4 ESV_000058 0.02152854 Eukaryota Chordata Actinopteri
8         8 ESV_000811 0.01747658 Eukaryota Chordata Actinopteri
9        10 ESV_037451 0.01209580 Eukaryota Chordata Actinopteri
10        9 ESV_041012 0.01530958 Eukaryota Chordata Actinopteri
             Order       Family         Genus                   Species
1      Spariformes  Lethrinidae     Lethrinus       Lethrinus obsoletus
2  Acanthuriformes Acanthuridae  Ctenochaetus     Ctenochaetus striatus
3   Atheriniformes  Atherinidae  Hypoatherina Hypoatherina celebesensis
4     Clupeiformes    Clupeidae Spratelloides Spratelloides delicatulus
5  Acanthuriformes Acanthuridae    Acanthurus       Acanthurus lineatus
6    Lutjaniformes   Lutjanidae        Caesio             Caesio cuning
7     Beloniformes    Belonidae     Tylosurus            Tylosurus acus
8    Lutjaniformes   Lutjanidae   Pterocaesio          Pterocaesio tile
9      Spariformes  Lethrinidae     Monotaxis     Monotaxis grandoculis
10     Kurtiformes   Apogonidae       Verulux        Verulux cypselurus

Top Offshore Species

$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 11 taxa and 88 samples ]
sample_data() Sample Data:       [ 88 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 11 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid  abundance   Kingdom   Phylum       Class
1         1 ESV_041947 0.09850082 Eukaryota Chordata Actinopteri
2         2 ESV_033752 0.06253358 Eukaryota Chordata Actinopteri
3         5 ESV_000044 0.03510401 Eukaryota Chordata Actinopteri
4         7 ESV_001029 0.02361620 Eukaryota Chordata Actinopteri
5         4 ESV_042017 0.03529597 Eukaryota Chordata Actinopteri
6         3 ESV_000892 0.04693707 Eukaryota Chordata Actinopteri
7         8 ESV_040493 0.02287200 Eukaryota Chordata Actinopteri
8         6 ESV_033648 0.02791025 Eukaryota Chordata Actinopteri
9        10 ESV_041165 0.01359034 Eukaryota Chordata Actinopteri
10        9 ESV_000858 0.02016873 Eukaryota Chordata Actinopteri
             Order        Family          Genus                      Species
1   Myctophiformes   Myctophidae      Myctophum         Myctophum lychnobium
2     Beloniformes   Exocoetidae      Exocoetus           Exocoetus volitans
3    Carangiformes    Carangidae     Decapterus        Decapterus macarellus
4    Scombriformes    Scombridae     Katsuwonus           Katsuwonus pelamis
5     Beloniformes   Exocoetidae   Prognichthys          Prognichthys sealei
6    Carangiformes    Carangidae          Selar       Selar crumenophthalmus
7   Myctophiformes   Myctophidae  Symbolophorus      Symbolophorus evermanni
8     Beloniformes Hemiramphidae  Oxyporhamphus    Oxyporhamphus micropterus
9     Beloniformes   Exocoetidae    Cheilopogon       Cheilopogon atrisignis
10 Syngnathiformes      Mullidae Mulloidichthys Mulloidichthys flavolineatus

###To convert phyloseq object to dataframe use metagMisc

###Species per Zone

$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 31 taxa and 19 samples ]
sample_data() Sample Data:       [ 19 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 31 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid   abundance   Kingdom   Phylum       Class
1         1 ESV_040600 0.094671627 Eukaryota Chordata Actinopteri
2        17 ESV_000147 0.011740314 Eukaryota Chordata Actinopteri
3         2 ESV_040410 0.036503437 Eukaryota Chordata Actinopteri
4        13 ESV_039694 0.018609195 Eukaryota Chordata Actinopteri
5         4 ESV_041619 0.033317884 Eukaryota Chordata Actinopteri
6        24 ESV_001422 0.008475250 Eukaryota Chordata Actinopteri
7         5 ESV_000058 0.033276472 Eukaryota Chordata Actinopteri
8         3 ESV_040447 0.034589830 Eukaryota Chordata Actinopteri
9        11 ESV_037451 0.019796357 Eukaryota Chordata Actinopteri
10       27 ESV_000858 0.007928621 Eukaryota Chordata Actinopteri
11       10 ESV_040361 0.020109935 Eukaryota Chordata Actinopteri
12        7 ESV_039690 0.028623292 Eukaryota Chordata Actinopteri
13       14 ESV_041905 0.014323267 Eukaryota Chordata Actinopteri
14       15 ESV_000785 0.013268477 Eukaryota Chordata Actinopteri
15        9 ESV_040601 0.020685553 Eukaryota Chordata Actinopteri
16       20 ESV_040472 0.010521667 Eukaryota Chordata Actinopteri
17       16 ESV_040646 0.012262224 Eukaryota Chordata Actinopteri
18       26 ESV_001115 0.008303651 Eukaryota Chordata Actinopteri
19       12 ESV_040715 0.018717976 Eukaryota Chordata Actinopteri
20       18 ESV_041621 0.010764927 Eukaryota Chordata Actinopteri
21       25 ESV_000257 0.008367862 Eukaryota Chordata Actinopteri
22        6 ESV_040360 0.029236088 Eukaryota Chordata Actinopteri
23       19 ESV_040413 0.010535890 Eukaryota Chordata Actinopteri
24        8 ESV_039681 0.023038233 Eukaryota Chordata Actinopteri
25       29 ESV_040608 0.007109750 Eukaryota Chordata Actinopteri
26       23 ESV_041880 0.009173407 Eukaryota Chordata Actinopteri
27       21 ESV_041044 0.010219800 Eukaryota Chordata Actinopteri
28       22 ESV_001324 0.009513420 Eukaryota Chordata Actinopteri
29       28 ESV_002221 0.007210750 Eukaryota Chordata Actinopteri
30       30 ESV_041134 0.006294702 Eukaryota Chordata Actinopteri
               Order        Family           Genus
1        Spariformes   Lethrinidae       Lethrinus
2    Acanthuriformes  Acanthuridae    Ctenochaetus
3     Atheriniformes   Atherinidae    Hypoatherina
4       Clupeiformes     Clupeidae   Spratelloides
5       Gerreiformes     Gerreidae          Gerres
6      Lutjaniformes    Lutjanidae          Caesio
7       Beloniformes     Belonidae       Tylosurus
8       Beloniformes Hemiramphidae     Hemiramphus
9        Spariformes   Lethrinidae       Monotaxis
10   Syngnathiformes      Mullidae  Mulloidichthys
11       Labriformes      Labridae       Choerodon
12         unk_order Pomacentridae  Neopomacentrus
13       Gobiiformes    Eleotridae           Butis
14      Mugiliformes     Mugilidae           Mugil
15       Gobiiformes      Gobiidae   Asterropteryx
16       Kurtiformes    Apogonidae         Verulux
17       Spariformes   Lethrinidae       Lethrinus
18  Holocentriformes Holocentridae     Myripristis
19         unk_order Pomacentridae Hemiglyphidodon
20     Lutjaniformes    Haemulidae  Plectorhinchus
21   Acanthuriformes  Acanthuridae      Acanthurus
22         unk_order Pomacentridae     Cheiloprion
23    Atheriniformes   Atherinidae   Atherinomorus
24      Clupeiformes     Clupeidae Herklotsichthys
25   Syngnathiformes      Mullidae      Parupeneus
26 Tetraodontiformes Monacanthidae        Pervagor
27       Gobiiformes      Gobiidae          Eviota
28         unk_order  Sphyraenidae       Sphyraena
29       Labriformes      Labridae     Leptoscarus
30   Syngnathiformes Callionymidae     Callionymus
                           Species
1              Lethrinus obsoletus
2            Ctenochaetus striatus
3        Hypoatherina celebesensis
4        Spratelloides delicatulus
5               Gerres erythrourus
6                    Caesio cuning
7                   Tylosurus acus
8                  Hemiramphus far
9            Monotaxis grandoculis
10    Mulloidichthys flavolineatus
11             Choerodon anchorago
12          Neopomacentrus nemurus
13                     Butis butis
14                  Mugil cephalus
15      Asterropteryx semipunctata
16              Verulux cypselurus
17                 Lethrinus harak
18            Myripristis violacea
19   Hemiglyphidodon plagiometopon
20          Plectorhinchus schotaf
21           Acanthurus nigricauda
22            Cheiloprion labiatus
23       Atherinomorus sp. OCNSW33
24 Herklotsichthys quadrimaculatus
25              Parupeneus indicus
26          Pervagor nigrolineatus
27               Eviota bifasciata
28              Sphyraena obtusata
29           Leptoscarus vaigienis
30           Callionymus enneactis
$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 31 taxa and 19 samples ]
sample_data() Sample Data:       [ 19 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 31 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid   abundance   Kingdom   Phylum       Class
1         1 ESV_000147 0.052428145 Eukaryota Chordata Actinopteri
2        14 ESV_039694 0.013843405 Eukaryota Chordata Actinopteri
3         5 ESV_000812 0.022882768 Eukaryota Chordata Actinopteri
4         2 ESV_040968 0.036617345 Eukaryota Chordata Actinopteri
5         9 ESV_001422 0.017431683 Eukaryota Chordata Actinopteri
6         3 ESV_040477 0.028095075 Eukaryota Chordata Actinopteri
7         6 ESV_040466 0.020167888 Eukaryota Chordata Actinopteri
8        24 ESV_039690 0.006737800 Eukaryota Chordata Actinopteri
9         4 ESV_040382 0.025863462 Eukaryota Chordata Actinopteri
10       18 ESV_040357 0.008345889 Eukaryota Chordata Actinopteri
11       30 ESV_040472 0.005577037 Eukaryota Chordata Actinopteri
12       11 ESV_001611 0.016615620 Eukaryota Chordata Actinopteri
13       27 ESV_001033 0.005803034 Eukaryota Chordata Actinopteri
14       10 ESV_041822 0.016739567 Eukaryota Chordata Actinopteri
15        8 ESV_000028 0.018323410 Eukaryota Chordata Actinopteri
16       26 ESV_000257 0.005852212 Eukaryota Chordata Actinopteri
17       21 ESV_040474 0.007468086 Eukaryota Chordata Actinopteri
18       16 ESV_000001 0.011867045 Eukaryota Chordata Actinopteri
19       15 ESV_000155 0.013280730 Eukaryota Chordata Actinopteri
20       12 ESV_040444 0.014820397 Eukaryota Chordata Actinopteri
21       20 ESV_001832 0.007697158 Eukaryota Chordata Actinopteri
22        7 ESV_001639 0.019124669 Eukaryota Chordata Actinopteri
23       23 ESV_040383 0.007239178 Eukaryota Chordata Actinopteri
24       17 ESV_000932 0.008936700 Eukaryota Chordata Actinopteri
25       13 ESV_040443 0.014063872 Eukaryota Chordata Actinopteri
26       19 ESV_039693 0.007875896 Eukaryota Chordata Actinopteri
27       29 ESV_000250 0.005579969 Eukaryota Chordata Actinopteri
28       25 ESV_036258 0.006079955 Eukaryota Chordata Actinopteri
29       28 ESV_040950 0.005646821 Eukaryota Chordata Actinopteri
30       22 ESV_000971 0.007353144 Eukaryota Chordata Actinopteri
               Order         Family          Genus
1    Acanthuriformes   Acanthuridae   Ctenochaetus
2       Clupeiformes      Clupeidae  Spratelloides
3    Acanthuriformes   Acanthuridae     Acanthurus
4        Gobiiformes       Gobiidae    Callogobius
5      Lutjaniformes     Lutjanidae         Caesio
6          unk_order  Pomacentridae    Pomacentrus
7      Carangiformes     Carangidae     Megalaspis
8          unk_order  Pomacentridae Neopomacentrus
9        Kurtiformes     Apogonidae        Zoramia
10     Lutjaniformes     Lutjanidae         Caesio
11       Kurtiformes     Apogonidae        Verulux
12       Spariformes    Lethrinidae      Monotaxis
13  Holocentriformes  Holocentridae    Myripristis
14   Syngnathiformes       Mullidae        Upeneus
15       Labriformes       Labridae     Thalassoma
16   Acanthuriformes   Acanthuridae     Acanthurus
17      Clupeiformes    Engraulidae Encrasicholina
18     Scombriformes     Scombridae      Euthynnus
19     Lutjaniformes     Lutjanidae       Lutjanus
20      Beloniformes  Hemiramphidae   Hyporhamphus
21     Scombriformes     Scombridae  Scomberomorus
22    Anguilliformes     Muraenidae    Gymnothorax
23       Gobiiformes       Gobiidae    Koumansetta
24   Acanthuriformes   Acanthuridae   Ctenochaetus
25       Perciformes       Percidae         Sander
26     Blenniiformes     Blenniidae       Ecsenius
27       Labriformes       Labridae      Chlorurus
28 Chaetodontiformes Chaetodontidae      Chaetodon
29       Kurtiformes     Apogonidae      Pristicon
30     Lutjaniformes     Lutjanidae    Pterocaesio
                         Species
1          Ctenochaetus striatus
2      Spratelloides delicatulus
3            Acanthurus lineatus
4  Callogobius sp. 'misuji-haze'
5                  Caesio cuning
6          Pomacentrus burroughi
7             Megalaspis cordyla
8         Neopomacentrus nemurus
9           Zoramia viridiventer
10            Caesio caerulaurea
11            Verulux cypselurus
12         Monotaxis grandoculis
13       Myripristis greenfieldi
14            Upeneus sulphureus
15      Thalassoma amblycephalum
16         Acanthurus nigricauda
17     Encrasicholina heteroloba
18             Euthynnus affinis
19                Lutjanus bohar
20             Hyporhamphus yuri
21        Scomberomorus sinensis
22       Gymnothorax chilospilus
23           Koumansetta hectori
24        Ctenochaetus binotatus
25                Sander vitreus
26         Ecsenius yaeyamaensis
27            Chlorurus sordidus
28           Chaetodon ephippium
29         Pristicon rhodopterus
30              Pterocaesio tile
$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 31 taxa and 20 samples ]
sample_data() Sample Data:       [ 20 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 31 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid   abundance   Kingdom   Phylum       Class
1        19 ESV_001029 0.007745421 Eukaryota Chordata Actinopteri
2         4 ESV_000147 0.032571777 Eukaryota Chordata Actinopteri
3        10 ESV_040410 0.019725661 Eukaryota Chordata Actinopteri
4         7 ESV_039694 0.028473734 Eukaryota Chordata Actinopteri
5         2 ESV_000812 0.036548516 Eukaryota Chordata Actinopteri
6         3 ESV_001422 0.032881086 Eukaryota Chordata Actinopteri
7         5 ESV_000058 0.030513667 Eukaryota Chordata Actinopteri
8         1 ESV_000811 0.043696610 Eukaryota Chordata Actinopteri
9        17 ESV_000858 0.008451429 Eukaryota Chordata Actinopteri
10       20 ESV_040466 0.007687058 Eukaryota Chordata Actinopteri
11        6 ESV_041012 0.029104017 Eukaryota Chordata Actinopteri
12        8 ESV_040357 0.025004504 Eukaryota Chordata Actinopteri
13       11 ESV_041240 0.019102107 Eukaryota Chordata Actinopteri
14        9 ESV_041164 0.022570746 Eukaryota Chordata Actinopteri
15       12 ESV_041391 0.017602345 Eukaryota Chordata Actinopteri
16       13 ESV_041788 0.016279054 Eukaryota Chordata Actinopteri
17       16 ESV_000090 0.009617720 Eukaryota Chordata Actinopteri
18       22 ESV_000889 0.007629874 Eukaryota Chordata Actinopteri
19       14 ESV_035276 0.013163266 Eukaryota Chordata Actinopteri
20       24 ESV_040577 0.007075792 Eukaryota Chordata Actinopteri
21       18 ESV_001470 0.008024543 Eukaryota Chordata Actinopteri
22       28 ESV_000917 0.006351470 Eukaryota Chordata Actinopteri
23       30 ESV_000264 0.006164827 Eukaryota Chordata Actinopteri
24       23 ESV_041100 0.007548079 Eukaryota Chordata Actinopteri
25       15 ESV_040540 0.011072667 Eukaryota Chordata Actinopteri
26       21 ESV_040515 0.007686028 Eukaryota Chordata Actinopteri
27       27 ESV_041440 0.006634949 Eukaryota Chordata Actinopteri
28       26 ESV_000905 0.006763543 Eukaryota Chordata Actinopteri
29       29 ESV_040507 0.006199564 Eukaryota Chordata Actinopteri
30       25 ESV_004310 0.006825694 Eukaryota Chordata Actinopteri
              Order          Family          Genus
1     Scombriformes      Scombridae     Katsuwonus
2   Acanthuriformes    Acanthuridae   Ctenochaetus
3    Atheriniformes     Atherinidae   Hypoatherina
4      Clupeiformes       Clupeidae  Spratelloides
5   Acanthuriformes    Acanthuridae     Acanthurus
6     Lutjaniformes      Lutjanidae         Caesio
7      Beloniformes       Belonidae      Tylosurus
8     Lutjaniformes      Lutjanidae    Pterocaesio
9   Syngnathiformes        Mullidae Mulloidichthys
10    Carangiformes      Carangidae     Megalaspis
11      Kurtiformes      Apogonidae        Verulux
12    Lutjaniformes      Lutjanidae         Caesio
13    Lutjaniformes      Haemulidae Plectorhinchus
14   Myctophiformes     Myctophidae   Bolinichthys
15   Anguilliformes      Muraenidae    Gymnothorax
16      Gobiiformes        Gobiidae      Oplopomus
17  Acanthuriformes    Acanthuridae           Naso
18        unk_order       Siganidae        Siganus
19 Holocentriformes   Holocentridae    Myripristis
20   Atheriniformes     Atherinidae   Stenatherina
21      Perciformes      Serranidae   Plectropomus
22  Acanthuriformes    Acanthuridae           Naso
23      Perciformes      Serranidae  Cephalopholis
24      Gobiiformes        Gobiidae         Eviota
25   Myctophiformes     Myctophidae      Myctophum
26        unk_order Pseudochromidae  Pseudochromis
27   Anguilliformes      Muraenidae   Uropterygius
28 Gonorynchiformes        Chanidae         Chanos
29      Spariformes     Lethrinidae      Lethrinus
30     Beloniformes     Exocoetidae   Parexocoetus
                         Species
1             Katsuwonus pelamis
2          Ctenochaetus striatus
3      Hypoatherina celebesensis
4      Spratelloides delicatulus
5            Acanthurus lineatus
6                  Caesio cuning
7                 Tylosurus acus
8               Pterocaesio tile
9   Mulloidichthys flavolineatus
10            Megalaspis cordyla
11            Verulux cypselurus
12            Caesio caerulaurea
13 Plectorhinchus chaetodonoides
14         Bolinichthys longipes
15      Gymnothorax australicola
16           Oplopomus oplopomus
17                Naso lituratus
18             Siganus argenteus
19            Myripristis adusta
20         Stenatherina panatela
21        Plectropomus leopardus
22                Naso unicornis
23         Cephalopholis urodeta
24               Eviota shimadai
25      Myctophum sp. FLMOO_1333
26     Pseudochromis tapeinosoma
27     Uropterygius alboguttatus
28                 Chanos chanos
29         Lethrinus reticulatus
30            Parexocoetus mento
$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 31 taxa and 20 samples ]
sample_data() Sample Data:       [ 20 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 31 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid    abundance   Kingdom   Phylum       Class
1        10 ESV_041947 2.483473e-02 Eukaryota Chordata Actinopteri
2        14 ESV_033752 1.086079e-02 Eukaryota Chordata Actinopteri
3         2 ESV_000044 5.419745e-02 Eukaryota Chordata Actinopteri
4         1 ESV_001029 6.325538e-02 Eukaryota Chordata Actinopteri
5        24 ESV_009973 3.345648e-05 Eukaryota Chordata Actinopteri
6         7 ESV_042017 4.120595e-02 Eukaryota Chordata Actinopteri
7        19 ESV_000892 5.048579e-03 Eukaryota Chordata Actinopteri
8        15 ESV_040493 1.017009e-02 Eukaryota Chordata Actinopteri
9         8 ESV_033648 3.561386e-02 Eukaryota Chordata Actinopteri
10        6 ESV_041165 4.177431e-02 Eukaryota Chordata Actinopteri
11       11 ESV_042162 2.435473e-02 Eukaryota Chordata Actinopteri
12        4 ESV_000858 4.990566e-02 Eukaryota Chordata Actinopteri
13        9 ESV_010681 3.030887e-02 Eukaryota Chordata Actinopteri
14        5 ESV_001250 4.496012e-02 Eukaryota Chordata Actinopteri
15       16 ESV_034586 8.374150e-03 Eukaryota Chordata Actinopteri
16       17 ESV_001558 5.903726e-03 Eukaryota Chordata Actinopteri
17       22 ESV_000001 1.653418e-03 Eukaryota Chordata Actinopteri
18       13 ESV_007833 1.446092e-02 Eukaryota Chordata Actinopteri
19        3 ESV_010025 4.995450e-02 Eukaryota Chordata Actinopteri
20       12 ESV_033730 1.673379e-02 Eukaryota Chordata Actinopteri
21       23 ESV_040928 4.289117e-04 Eukaryota Chordata Actinopteri
22       20 ESV_035485 4.193432e-03 Eukaryota Chordata Actinopteri
23       21 ESV_032341 3.480903e-03 Eukaryota Chordata Actinopteri
24       18 ESV_002169 5.317640e-03 Eukaryota Chordata Actinopteri
25       27 ESV_000832 1.003697e-05 Eukaryota Chordata Actinopteri
26       25 ESV_018666 3.211844e-05 Eukaryota Chordata Actinopteri
27       26 ESV_001026 1.338285e-05 Eukaryota Chordata Actinopteri
28       30 ESV_041306 3.345690e-06 Eukaryota Chordata Actinopteri
29       28 ESV_001331 5.353247e-06 Eukaryota Chordata Actinopteri
30       29 ESV_001013 4.684091e-06 Eukaryota Chordata Actinopteri
                Order         Family          Genus
1      Myctophiformes    Myctophidae      Myctophum
2        Beloniformes    Exocoetidae      Exocoetus
3       Carangiformes     Carangidae     Decapterus
4       Scombriformes     Scombridae     Katsuwonus
5       Salmoniformes     Salmonidae   Oncorhynchus
6        Beloniformes    Exocoetidae   Prognichthys
7       Carangiformes     Carangidae          Selar
8      Myctophiformes    Myctophidae  Symbolophorus
9        Beloniformes  Hemiramphidae  Oxyporhamphus
10       Beloniformes    Exocoetidae    Cheilopogon
11     Myctophiformes    Myctophidae       Hygophum
12    Syngnathiformes       Mullidae Mulloidichthys
13 Cyprinodontiformes     Fundulidae       Fundulus
14    Acanthuriformes   Acanthuridae     Acanthurus
15       Beloniformes    Exocoetidae    Cheilopogon
16   Holocentriformes  Holocentridae    Myripristis
17      Scombriformes     Scombridae      Euthynnus
18       Clupeiformes      Clupeidae     Brevoortia
19       Clupeiformes    Engraulidae      Engraulis
20       Stomiiformes Phosichthyidae   Vinciguerria
21       Clupeiformes      Clupeidae    Amblygaster
22       Stomiiformes Gonostomatidae     Cyclothone
23      Cypriniformes  Nemacheilidae      Barbatula
24        Labriformes       Labridae         Scarus
25          unk_order  Pomacentridae        Chromis
26      Lutjaniformes     Lutjanidae       Lutjanus
27  Tetraodontiformes     Balistidae      Sufflamen
28     Atheriniformes       Isonidae            Iso
29   Centrarchiformes    Cirrhitidae      Cirrhitus
30   Centrarchiformes    Cirrhitidae Amblycirrhitus
                         Species
1           Myctophum lychnobium
2             Exocoetus volitans
3          Decapterus macarellus
4             Katsuwonus pelamis
5       Oncorhynchus tshawytscha
6            Prognichthys sealei
7         Selar crumenophthalmus
8        Symbolophorus evermanni
9      Oxyporhamphus micropterus
10        Cheilopogon atrisignis
11     Hygophum sp. CBM:ZF:14740
12  Mulloidichthys flavolineatus
13             Fundulus zebrinus
14         Acanthurus triostegus
15   Cheilopogon spilonotopterus
16           Myripristis vittata
17             Euthynnus affinis
18           Brevoortia tyrannus
19              Engraulis mordax
20 Vinciguerria sp. CBM:ZF:14736
21              Amblygaster sirm
22               Cyclothone alba
23           Barbatula barbatula
24              Scarus schlegeli
25           Chromis vanderbilti
26              Lutjanus kasmira
27               Sufflamen bursa
28                 Iso flosmaris
29          Cirrhitus pinnulatus
30       Amblycirrhitus bimacula
$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 33 taxa and 18 samples ]
sample_data() Sample Data:       [ 18 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 33 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid    abundance   Kingdom   Phylum       Class
1         1 ESV_033752 1.485672e-01 Eukaryota Chordata Actinopteri
2        30 ESV_000044 5.204407e-06 Eukaryota Chordata Actinopteri
3        11 ESV_001029 6.912847e-03 Eukaryota Chordata Actinopteri
4        23 ESV_009973 2.156049e-05 Eukaryota Chordata Actinopteri
5         6 ESV_042017 2.783733e-02 Eukaryota Chordata Actinopteri
6         2 ESV_000892 1.235262e-01 Eukaryota Chordata Actinopteri
7         9 ESV_033648 1.292620e-02 Eukaryota Chordata Actinopteri
8        19 ESV_000058 7.955201e-05 Eukaryota Chordata Actinopteri
9        10 ESV_042162 1.287347e-02 Eukaryota Chordata Actinopteri
10        3 ESV_041978 1.102212e-01 Eukaryota Chordata Actinopteri
11        4 ESV_001096 3.817902e-02 Eukaryota Chordata Actinopteri
12       14 ESV_001558 2.692909e-03 Eukaryota Chordata Actinopteri
13        8 ESV_035693 1.396640e-02 Eukaryota Chordata Actinopteri
14       31 ESV_000250 5.204407e-06 Eukaryota Chordata Actinopteri
15       26 ESV_004177 1.189579e-05 Eukaryota Chordata    Mammalia
16        5 ESV_027198 2.980896e-02 Eukaryota Chordata Actinopteri
17       15 ESV_042131 2.008158e-03 Eukaryota Chordata Actinopteri
18       12 ESV_000190 6.702443e-03 Eukaryota Chordata Actinopteri
19        7 ESV_040264 1.486676e-02 Eukaryota Chordata Actinopteri
20       13 ESV_042297 5.858675e-03 Eukaryota Chordata Actinopteri
21       16 ESV_003048 1.918939e-03 Eukaryota Chordata    Mammalia
22       27 ESV_025394 1.189573e-05 Eukaryota Chordata Actinopteri
23       18 ESV_030101 4.096557e-04 Eukaryota Chordata Actinopteri
24       17 ESV_042281 1.010385e-03 Eukaryota Chordata Actinopteri
25       24 ESV_000832 1.933053e-05 Eukaryota Chordata Actinopteri
26       29 ESV_018666 5.947893e-06 Eukaryota Chordata Actinopteri
27       22 ESV_001026 2.156070e-05 Eukaryota Chordata Actinopteri
28       25 ESV_018663 1.263927e-05 Eukaryota Chordata Actinopteri
29       20 ESV_042265 5.873466e-05 Eukaryota Chordata Actinopteri
30       32 ESV_009939 5.204407e-06 Eukaryota Chordata Actinopteri
31       21 ESV_001128 3.568736e-05 Eukaryota Chordata Actinopteri
32       28 ESV_009969 1.040840e-05 Eukaryota Chordata Actinopteri
                Order        Family         Genus                       Species
1        Beloniformes   Exocoetidae     Exocoetus            Exocoetus volitans
2       Carangiformes    Carangidae    Decapterus         Decapterus macarellus
3       Scombriformes    Scombridae    Katsuwonus            Katsuwonus pelamis
4       Salmoniformes    Salmonidae  Oncorhynchus      Oncorhynchus tshawytscha
5        Beloniformes   Exocoetidae  Prognichthys           Prognichthys sealei
6       Carangiformes    Carangidae         Selar        Selar crumenophthalmus
7        Beloniformes Hemiramphidae Oxyporhamphus     Oxyporhamphus micropterus
8        Beloniformes     Belonidae     Tylosurus                Tylosurus acus
9      Myctophiformes   Myctophidae      Hygophum     Hygophum sp. CBM:ZF:14740
10     Myctophiformes   Myctophidae     Myctophum          Myctophum lychnobium
11        Gobiiformes      Gobiidae  Ptereleotris      Ptereleotris heteroptera
12   Holocentriformes Holocentridae   Myripristis           Myripristis vittata
13    Syngnathiformes      Mullidae    Parupeneus         Parupeneus barberinus
14        Labriformes      Labridae     Chlorurus            Chlorurus sordidus
15       Artiodactyla   Delphinidae     Pseudorca          Pseudorca crassidens
16       Cichliformes     Cichlidae      Coptodon               Coptodon zillii
17     Myctophiformes   Myctophidae Symbolophorus       Symbolophorus evermanni
18   Holocentriformes Holocentridae   Myripristis         Myripristis chryseres
19     Anguilliformes    Muraenidae  Uropterygius      Uropterygius micropterus
20  Tetraodontiformes    Balistidae  Xanthichthys Xanthichthys caeruleolineatus
21       Artiodactyla   Delphinidae      Stenella         Stenella longirostris
22    Acanthuriformes  Acanthuridae    Acanthurus        Acanthurus nigrofuscus
23      Carangiformes Coryphaenidae    Coryphaena           Coryphaena hippurus
24      Blenniiformes      Clinidae     Gibbonsia       Gibbonsia montereyensis
25          unk_order Pomacentridae       Chromis           Chromis vanderbilti
26      Lutjaniformes    Lutjanidae      Lutjanus              Lutjanus kasmira
27  Tetraodontiformes    Balistidae     Sufflamen               Sufflamen bursa
28      Blenniiformes    Blenniidae   Cirripectes          Cirripectes imitator
29     Myctophiformes   Myctophidae       Diaphus        Diaphus brachycephalus
30      Salmoniformes    Salmonidae  Oncorhynchus          Oncorhynchus kisutch
31    Syngnathiformes      Mullidae    Parupeneus        Parupeneus cyclostomus
32 Cyprinodontiformes    Fundulidae      Fundulus         Fundulus heteroclitus
$ps_obj
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 31 taxa and 50 samples ]
sample_data() Sample Data:       [ 50 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 31 taxa by 7 taxonomic ranks ]

$top_taxa
   tax_rank      taxid   abundance   Kingdom   Phylum       Class
1         1 ESV_041947 0.123747900 Eukaryota Chordata Actinopteri
2         2 ESV_033752 0.052230587 Eukaryota Chordata Actinopteri
3         3 ESV_000044 0.040102201 Eukaryota Chordata Actinopteri
4        12 ESV_001029 0.013773734 Eukaryota Chordata Actinopteri
5         5 ESV_042017 0.035617085 Eukaryota Chordata Actinopteri
6         4 ESV_000892 0.036120372 Eukaryota Chordata Actinopteri
7         6 ESV_040493 0.035463741 Eukaryota Chordata Actinopteri
8         7 ESV_033648 0.030223059 Eukaryota Chordata Actinopteri
9        19 ESV_041165 0.007209281 Eukaryota Chordata Actinopteri
10        9 ESV_000858 0.015534708 Eukaryota Chordata Actinopteri
11       14 ESV_038744 0.012359759 Eukaryota Chordata Actinopteri
12       10 ESV_000827 0.015301911 Eukaryota Chordata Actinopteri
13       15 ESV_012590 0.011680251 Eukaryota Chordata Actinopteri
14       18 ESV_000983 0.008350039 Eukaryota Chordata Actinopteri
15       22 ESV_025924 0.006833146 Eukaryota Chordata Actinopteri
16       17 ESV_042383 0.010068654 Eukaryota Chordata Actinopteri
17        8 ESV_040500 0.017601006 Eukaryota Chordata Actinopteri
18       30 ESV_009176 0.002875114 Eukaryota Chordata Actinopteri
19       21 ESV_042001 0.006922459 Eukaryota Chordata Actinopteri
20       23 ESV_042499 0.006671128 Eukaryota Chordata Actinopteri
21       11 ESV_042360 0.014917831 Eukaryota Chordata Actinopteri
22       13 ESV_041088 0.013165591 Eukaryota Chordata Actinopteri
23       26 ESV_042500 0.005613340 Eukaryota Chordata Actinopteri
24       28 ESV_040333 0.004698089 Eukaryota Chordata Actinopteri
25       20 ESV_033582 0.007112842 Eukaryota Chordata Actinopteri
26       29 ESV_042002 0.003159444 Eukaryota Chordata Actinopteri
27       25 ESV_004177 0.006245652 Eukaryota Chordata    Mammalia
28       16 ESV_042048 0.010494225 Eukaryota Chordata Actinopteri
29       24 ESV_040064 0.006645879 Eukaryota Chordata Actinopteri
30       27 ESV_015212 0.004845362 Eukaryota Chordata Actinopteri
             Order        Family          Genus                      Species
1   Myctophiformes   Myctophidae      Myctophum         Myctophum lychnobium
2     Beloniformes   Exocoetidae      Exocoetus           Exocoetus volitans
3    Carangiformes    Carangidae     Decapterus        Decapterus macarellus
4    Scombriformes    Scombridae     Katsuwonus           Katsuwonus pelamis
5     Beloniformes   Exocoetidae   Prognichthys          Prognichthys sealei
6    Carangiformes    Carangidae          Selar       Selar crumenophthalmus
7   Myctophiformes   Myctophidae  Symbolophorus      Symbolophorus evermanni
8     Beloniformes Hemiramphidae  Oxyporhamphus    Oxyporhamphus micropterus
9     Beloniformes   Exocoetidae    Cheilopogon       Cheilopogon atrisignis
10 Syngnathiformes      Mullidae Mulloidichthys Mulloidichthys flavolineatus
11   Scombriformes    Gempylidae       Gempylus             Gempylus serpens
12     Gobiiformes      Gobiidae    Microgobius      Microgobius thalassinus
13   Cypriniformes   Leuciscidae       Couesius            Couesius plumbeus
14   Ephippiformes    Ephippidae Chaetodipterus         Chaetodipterus faber
15   Cypriniformes    Gobionidae          Gobio                  Gobio gobio
16  Myctophiformes   Myctophidae      Myctophum      Myctophum brachygnathum
17    Mugiliformes     Mugilidae          Mugil               Mugil cephalus
18       unk_order     Moronidae         Morone             Morone americana
19   Carangiformes    Carangidae     Decapterus          Decapterus muroadsi
20    Gerreiformes     Gerreidae       Eugerres            Eugerres plumieri
21  Myctophiformes   Myctophidae Centrobranchus       Centrobranchus andreae
22   Carangiformes    Carangidae         Caranx             Caranx papuensis
23   Scombriformes      Bramidae       Taractes           Taractes rubescens
24 Syngnathiformes Callionymidae    Callionymus     Callionymus marquesensis
25  Myctophiformes   Myctophidae        Diaphus           Diaphus splendidus
26    Beloniformes   Exocoetidae     Cypselurus       Cypselurus angusticeps
27    Artiodactyla   Delphinidae      Pseudorca         Pseudorca crassidens
28  Myctophiformes   Myctophidae      Lampadena           Lampadena luminosa
29     Spariformes      Sparidae        Lagodon           Lagodon rhomboides
30   Cypriniformes   Leuciscidae     Cyprinella        Cyprinella spiloptera